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@article{DBLP:journals/jcamd/AbdoGAP20, author = {Ammar Abdo and Eissa Ghaleb and Naser K. A. Alajmi and Maude Pupin}, title = {Monomer structure fingerprints: an extension of the monomer composition version for peptide databases}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {11}, pages = {1147--1156}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00336-8}, doi = {10.1007/S10822-020-00336-8}, timestamp = {Tue, 29 Dec 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/jcamd/AbdoGAP20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/AghazadehKRB20, author = {Hossein Aghazadeh and Mokhtar Ganjali Koli and Reza Ranjbar and Kamran Pooshang Bagheri}, title = {Interactions of {GF-17} derived from {LL-37} antimicrobial peptide with bacterial membranes: a molecular dynamics simulation study}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {12}, pages = {1261--1273}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00348-4}, doi = {10.1007/S10822-020-00348-4}, timestamp = {Tue, 21 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/jcamd/AghazadehKRB20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/ArifAAFLY20, author = {Muhammad Arif and Saeed Ahmad and Farman Ali and Ge Fang and Min Li and Dong{-}Jun Yu}, title = {TargetCPP: accurate prediction of cell-penetrating peptides from optimized multi-scale features using gradient boost decision tree}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {8}, pages = {841--856}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00307-z}, doi = {10.1007/S10822-020-00307-Z}, timestamp = {Sun, 30 Jul 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/ArifAAFLY20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/ArslanFA20, author = {Evrim Arslan and Basak Koca Findik and Viktorya Aviyente}, title = {A blind {SAMPL6} challenge: insight into the octanol-water partition coefficients of drug-like molecules via a {DFT} approach}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {4}, pages = {463--470}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00284-3}, doi = {10.1007/S10822-020-00284-3}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/ArslanFA20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/AshidaK20, author = {Takeshi Ashida and Takeshi Kikuchi}, title = {A new method for estimating the relative binding free energy, derived from a free energy variational principle for the Pim-1-kinase-ligand and FKBP-ligand systems}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {6}, pages = {647--658}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00302-4}, doi = {10.1007/S10822-020-00302-4}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/AshidaK20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/AtanasioDR20, author = {Silvia Atanasio and Giuseppe Deganutti and Christopher A. Reynolds}, title = {Addressing free fatty acid receptor 1 {(FFAR1)} activation using supervised molecular dynamics}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {11}, pages = {1181--1193}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00338-6}, doi = {10.1007/S10822-020-00338-6}, timestamp = {Fri, 25 Dec 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/jcamd/AtanasioDR20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/BasciuKMBV20, author = {Andrea Basciu and Panagiotis I. Koukos and Giuliano Malloci and Alexandre M. J. J. Bonvin and Attilio Vittorio Vargiu}, title = {Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the {D3R} Grand Challenge 4}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {2}, pages = {149--162}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00244-6}, doi = {10.1007/S10822-019-00244-6}, timestamp = {Thu, 14 Oct 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/BasciuKMBV20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/BaumgartnerE20, author = {Matthew P. Baumgartner and David A. Evans}, title = {Side chain virtual screening of matched molecular pairs: a PDB-wide and ChEMBL-wide analysis}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {9}, pages = {953--963}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00313-1}, doi = {10.1007/S10822-020-00313-1}, timestamp = {Thu, 13 Aug 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/BaumgartnerE20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/BelgamoAPRRTCF20, author = {Juli{\'{a}}n A. B{\'{e}}lgamo and Lucas N. Alberca and Jorge L. P{\'{o}}rfido and Franco N. Caram Romero and Santiago Rodriguez and Alan Talevi and Betina C{\'{o}}rsico and Gisela R. Franchini}, title = {Application of target repositioning and in silico screening to exploit fatty acid binding proteins (FABPs) from Echinococcus multilocularis as possible drug targets}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {12}, pages = {1275--1288}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00352-8}, doi = {10.1007/S10822-020-00352-8}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/BelgamoAPRRTCF20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/BelloGR20, author = {Martiniano Bello and Concepci{\'{o}}n Guadarrama{-}Garc{\'{\i}}a and Rolando Alberto Rodriguez{-}Fonseca}, title = {Dissecting the molecular recognition of dual lapatinib derivatives for {EGFR/HER2}}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {3}, pages = {293--303}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00270-4}, doi = {10.1007/S10822-019-00270-4}, timestamp = {Thu, 14 Oct 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/BelloGR20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/BorioniCPMPPG20, author = {Jos{\'{e}} L. Borioni and Valeria Cavallaro and Adriana B. Pierini and Ana Paula Murray and Alicia B. Pe{\~{n}}{\'{e}}{\~{n}}ory and Marcelo Puiatti and Manuela E. Garc{\'{\i}}a}, title = {An activity prediction model for steroidal and triterpenoidal inhibitors of Acetylcholinesterase enzyme}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {10}, pages = {1079--1090}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00324-y}, doi = {10.1007/S10822-020-00324-Y}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/BorioniCPMPPG20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/BrownELLRS20, author = {Nathan Brown and Peter Ertl and Richard A. Lewis and Torsten Luksch and Daniel Reker and Nadine Schneider}, title = {Artificial intelligence in chemistry and drug design}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {7}, pages = {709--715}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00317-x}, doi = {10.1007/S10822-020-00317-X}, timestamp = {Thu, 14 Oct 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/BrownELLRS20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/BufanoLBLNSBC20, author = {Marianna Bufano and Marion Laudette and Jean{-}Paul Blondeau and Frank Lezoualc'h and Marianna Nalli and Romano Silvestri and Andrea Brancale and Antonio Coluccia}, title = {Modeling Epac1 interactions with the allosteric inhibitor {AM-001} by co-solvent molecular dynamics}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {11}, pages = {1171--1179}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00332-y}, doi = {10.1007/S10822-020-00332-Y}, timestamp = {Fri, 14 May 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/BufanoLBLNSBC20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/CharoenkwanNHS20, author = {Phasit Charoenkwan and Chanin Nantasenamat and Md. Mehedi Hasan and Watshara Shoombuatong}, title = {Meta-iPVP: a sequence-based meta-predictor for improving the prediction of phage virion proteins using effective feature representation}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {10}, pages = {1105--1116}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00323-z}, doi = {10.1007/S10822-020-00323-Z}, timestamp = {Sun, 25 Jul 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/CharoenkwanNHS20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/ChenWSPY20, author = {Jianzhong Chen and Wei Wang and Haibo Sun and Laixue Pang and Baohua Yin}, title = {Mutation-mediated influences on binding of anaplastic lymphoma kinase to crizotinib decoded by multiple replica Gaussian accelerated molecular dynamics}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {12}, pages = {1289--1305}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00355-5}, doi = {10.1007/S10822-020-00355-5}, timestamp = {Fri, 25 Dec 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/jcamd/ChenWSPY20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/ClarkMCLPRLFGGW20, author = {Robert D. Clark and Denise N. Morris and Gary Chinigo and Michael S. Lawless and Jacques Prudhomme and Karine G. Le Roch and Maria Jos{\'{e}} Lafuente and Santiago Ferrer and Francisco Javier Gamo and Robert Gadwood and Walter S. Woltosz}, title = {Design and tests of prospective property predictions for novel antimalarial 2-aminopropylaminoquinolones}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {11}, pages = {1117--1132}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00333-x}, doi = {10.1007/S10822-020-00333-X}, timestamp = {Fri, 25 Dec 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/jcamd/ClarkMCLPRLFGGW20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/ColodetteFMFSB20, author = {Natalie M. Colodette and Lucas S. Franco and Rodolfo C. Maia and Harold H. Fokoue and Carlos Mauricio R. Sant'Anna and Eliezer J. Barreiro}, title = {Novel phosphatidylinositol 4-kinases {III} beta (PI4KIII{\(\beta\)}) inhibitors discovered by virtual screening using free energy models}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {10}, pages = {1091--1103}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00327-9}, doi = {10.1007/S10822-020-00327-9}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/ColodetteFMFSB20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/DingXQCZHSH20, author = {Ye Ding and You Xu and Cheng Qian and Jinfeng Chen and Jian Zhu and Houhou Huang and Yi Shi and Jing Huang}, title = {Predicting partition coefficients of drug-like molecules in the {SAMPL6} challenge with Drude polarizable force fields}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {4}, pages = {421--435}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00282-5}, doi = {10.1007/S10822-020-00282-5}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/DingXQCZHSH20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/FanIB20, author = {Shujie Fan and Bogdan I. Iorga and Oliver Beckstein}, title = {Prediction of octanol-water partition coefficients for the SAMPL6-log {P} molecules using molecular dynamics simulations with OPLS-AA, {AMBER} and {CHARMM} force fields}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {5}, pages = {543--560}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00267-z}, doi = {10.1007/S10822-019-00267-Z}, timestamp = {Thu, 14 Oct 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/FanIB20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/GarciaTHG20, author = {Gonzalo Cerruela Garc{\'{\i}}a and Jos{\'{e}} P{\'{e}}rez{-}Parras Toledano and Aida de Haro{-}Garc{\'{\i}}a and Nicol{\'{a}}s Garc{\'{\i}}a{-}Pedrajas}, title = {Influence of feature rankers in the construction of molecular activity prediction models}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {3}, pages = {305--325}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00273-1}, doi = {10.1007/S10822-019-00273-1}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/GarciaTHG20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/GhiandoniBCHWWG20, author = {Gian Marco Ghiandoni and Michael J. Bodkin and Beining Chen and Dimitar Hristozov and James E. A. Wallace and James Webster and Valerie J. Gillet}, title = {Enhancing reaction-based de novo design using a multi-label reaction class recommender}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {7}, pages = {783--803}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00300-6}, doi = {10.1007/S10822-020-00300-6}, timestamp = {Wed, 07 Dec 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/jcamd/GhiandoniBCHWWG20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/GilsonA20, author = {Michael K. Gilson and Rommie E. Amaro}, title = {Drug Design Data Resource, Grand Challenge 4, second of two issues}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {2}, pages = {97}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00296-z}, doi = {10.1007/S10822-020-00296-Z}, timestamp = {Mon, 05 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/jcamd/GilsonA20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/GreenPLSMMBPM20, author = {Darren V. S. Green and Stephen D. Pickett and Christopher N. Luscombe and Stefan Senger and David Marcus and Jamel Meslamani and David Brett and Adam Powell and Jonathan Masson}, title = {{BRADSHAW:} a system for automated molecular design}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {7}, pages = {747--765}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00234-8}, doi = {10.1007/S10822-019-00234-8}, timestamp = {Fri, 14 May 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/GreenPLSMMBPM20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/GreenPLSMMBPM20a, author = {Darren V. S. Green and Stephen D. Pickett and Christopher N. Luscombe and Stefan Senger and David Marcus and Jamel Meslamani and David Brett and Adam Powell and Jonathan Masson}, title = {Correction to: {BRADSHAW:} a system for automated molecular design}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {7}, pages = {767}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00243-7}, doi = {10.1007/S10822-019-00243-7}, timestamp = {Thu, 14 Oct 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/GreenPLSMMBPM20a.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/GuanLM20, author = {Davy Guan and Raymond Lui and Slade Matthews}, title = {LogP prediction performance with the {SMD} solvation model and the {M06} density functional family for {SAMPL6} blind prediction challenge molecules}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {5}, pages = {511--522}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00278-1}, doi = {10.1007/S10822-020-00278-1}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/GuanLM20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/GunnerMRIC20, author = {Marilyn R. Gunner and Taichi Murakami and Ari{\"{e}}n S. Rustenburg and Mehtap Isik and John D. Chodera}, title = {Standard state free energies, not pK\({}_{\mbox{a}}\)s, are ideal for describing small molecule protonation and tautomeric states}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {5}, pages = {561--573}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00280-7}, doi = {10.1007/S10822-020-00280-7}, timestamp = {Mon, 15 Jun 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/GunnerMRIC20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/GureevNGVGT20, author = {Maxim Gureev and Daria Novikova and Tatyana Grigoreva and Svetlana Vorona and Alexander Garabadzhiu and Vyacheslav Tribulovich}, title = {Simulation of {MDM2} N-terminal domain conformational lability in the presence of imidazoline based inhibitors of MDM2-p53 protein-protein interaction}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {1}, pages = {55--70}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00260-6}, doi = {10.1007/S10822-019-00260-6}, timestamp = {Thu, 14 Oct 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/GureevNGVGT20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/HanpaiboolLTR20, author = {Chonnikan Hanpaibool and Matina Leelawiwat and Kaito Takahashi and Thanyada Rungrotmongkol}, title = {Source of oseltamivir resistance due to single {E119D} and double {E119D/H274Y} mutations in pdm09H1N1 influenza neuraminidase}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {1}, pages = {27--37}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00251-7}, doi = {10.1007/S10822-019-00251-7}, timestamp = {Mon, 26 Oct 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/jcamd/HanpaiboolLTR20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/HuB20, author = {Huabin Hu and J{\"{u}}rgen Bajorath}, title = {Simplified activity cliff network representations with high interpretability and immediate access to {SAR} information}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {9}, pages = {943--952}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00319-9}, doi = {10.1007/S10822-020-00319-9}, timestamp = {Fri, 14 May 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/HuB20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/IsikBFRCM20, author = {Mehtap Isik and Teresa Danielle Bergazin and Thomas Fox and Andrea Rizzi and John D. Chodera and David L. Mobley}, title = {Assessing the accuracy of octanol-water partition coefficient predictions in the {SAMPL6} Part {II} log {P} Challenge}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {4}, pages = {335--370}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00295-0}, doi = {10.1007/S10822-020-00295-0}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/IsikBFRCM20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/IsikLMRC20, author = {Mehtap Isik and Dorothy Levorse and David L. Mobley and Timothy Rhodes and John D. Chodera}, title = {Octanol-water partition coefficient measurements for the {SAMPL6} blind prediction challenge}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {4}, pages = {405--420}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00271-3}, doi = {10.1007/S10822-019-00271-3}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/IsikLMRC20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/JonesB20, author = {Michael R. Jones and Bernard R. Brooks}, title = {Quantum chemical predictions of water-octanol partition coefficients applied to the {SAMPL6} logP blind challenge}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {5}, pages = {485--493}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00286-1}, doi = {10.1007/S10822-020-00286-1}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/JonesB20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/KadukovaCG20, author = {Maria Kadukova and Vladimir Chupin and Sergei Grudinin}, title = {Docking rigid macrocycles using Convex-PL, AutoDock Vina, and RDKit in the {D3R} Grand Challenge 4}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {2}, pages = {191--200}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00263-3}, doi = {10.1007/S10822-019-00263-3}, timestamp = {Mon, 26 Oct 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/jcamd/KadukovaCG20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/KhannaMDP20, author = {Vikram Khanna and Jacob I. Monroe and Michael F. Doherty and Baron Peters}, title = {Performing solvation free energy calculations in {LAMMPS} using the decoupling approach}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {6}, pages = {641--646}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00303-3}, doi = {10.1007/S10822-020-00303-3}, timestamp = {Mon, 15 Jun 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/KhannaMDP20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/KhatunHSK20, author = {Mst. Shamima Khatun and Md. Mehedi Hasan and Watshara Shoombuatong and Hiroyuki Kurata}, title = {ProIn-Fuse: improved and robust prediction of proinflammatory peptides by fusing of multiple feature representations}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {12}, pages = {1229--1236}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00343-9}, doi = {10.1007/S10822-020-00343-9}, timestamp = {Wed, 07 Apr 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/KhatunHSK20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/KotelnikovALIPB20, author = {Sergei Kotelnikov and Andrey Alekseenko and Cong Liu and Mikhail Ignatov and Dzmitry Padhorny and Emiliano Brini and Mark Lukin and Evangelos A. Coutsias and Ken A. Dill and Dima Kozakov}, title = {Sampling and refinement protocols for template-based macrocycle docking: 2018 {D3R} Grand Challenge 4}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {2}, pages = {179--189}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00257-1}, doi = {10.1007/S10822-019-00257-1}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/KotelnikovALIPB20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/KovarSPMSBKZB20, author = {Petr Kov{\'{a}}r and Jakub Skoda and Miroslav Posp{\'{\i}}sil and Kl{\'{a}}ra Mel{\'{a}}nov{\'{a}} and Jan Svoboda and Ludv{\'{\i}}k Benes and Petr Kut{\'{a}}lek and V{\'{\i}}tezslav Zima and Filip Bures}, title = {How N-(pyridin-4-yl)pyridin-4-amine and its methyl and nitro derivatives are arranged in the interlayer space of zirconium sulfophenylphosphonate: a problem solved by experimental and calculation methods}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {6}, pages = {683--695}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00299-w}, doi = {10.1007/S10822-020-00299-W}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/KovarSPMSBKZB20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/KramerHJB20, author = {Andreas Kr{\"{a}}mer and Phillip S. Hudson and Michael R. Jones and Bernard R. Brooks}, title = {Multi-phase Boltzmann weighting: accounting for local inhomogeneity in molecular simulations of water-octanol partition coefficients in the {SAMPL6} challenge}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {5}, pages = {471--483}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00285-2}, doi = {10.1007/S10822-020-00285-2}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/KramerHJB20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/KuderMKK20, author = {Kamil J. Kuder and Ilona Michalik and Katarzyna Kiec{-}Kononowicz and Peter Kolb}, title = {A Taxicab geometry quantification system to evaluate the performance of in silico methods: a case study on adenosine receptors ligands}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {6}, pages = {697--707}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00301-5}, doi = {10.1007/S10822-020-00301-5}, timestamp = {Fri, 14 May 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/KuderMKK20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/LansPCC20, author = {Isaias Lans and Karen Palacio{-}Rodr{\'{\i}}guez and Claudio N. Cavasotto and Pilar Cossio}, title = {Flexi-pharma: a molecule-ranking strategy for virtual screening using pharmacophores from ligand-free conformational ensembles}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {10}, pages = {1063--1077}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00329-7}, doi = {10.1007/S10822-020-00329-7}, timestamp = {Fri, 14 May 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/LansPCC20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/LinBHMV20, author = {Arkadii I. Lin and Bernd Beck and Dragos Horvath and Gilles Marcou and Alexandre Varnek}, title = {Diversifying chemical libraries with generative topographic mapping}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {7}, pages = {805--815}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00215-x}, doi = {10.1007/S10822-019-00215-X}, timestamp = {Sun, 12 Nov 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/jcamd/LinBHMV20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/LiuK20, author = {Kai Liu and Hironori Kokubo}, title = {Prediction of ligand binding mode among multiple cross-docking poses by molecular dynamics simulations}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {11}, pages = {1195--1205}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00340-y}, doi = {10.1007/S10822-020-00340-Y}, timestamp = {Fri, 25 Dec 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/jcamd/LiuK20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/Lopez-LopezROM20, author = {Edgar L{\'{o}}pez{-}L{\'{o}}pez and Obdulia Rabal and Julen Oyarzabal and Jos{\'{e}} L. Medina{-}Franco}, title = {Towards the understanding of the activity of G9a inhibitors: an activity landscape and molecular modeling approach}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {6}, pages = {659--669}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00298-x}, doi = {10.1007/S10822-020-00298-X}, timestamp = {Tue, 16 Jun 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/Lopez-LopezROM20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/LoschenRK20, author = {Christoph Loschen and Jens Reinisch and Andreas Klamt}, title = {{COSMO-RS} based predictions for the {SAMPL6} logP challenge}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {4}, pages = {385--392}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00259-z}, doi = {10.1007/S10822-019-00259-Z}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/LoschenRK20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/LuiGM20, author = {Raymond Lui and Davy Guan and Slade Matthews}, title = {A comparison of molecular representations for lipophilicity quantitative structure-property relationships with results from the {SAMPL6} logP Prediction Challenge}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {5}, pages = {523--534}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00279-0}, doi = {10.1007/S10822-020-00279-0}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/LuiGM20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/MagantiB20, author = {Lakshmi Maganti and Dhananjay Bhattacharyya}, title = {Sequence specificity in DNA-drug intercalation: {MD} simulation and density functional theory approaches}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {1}, pages = {83--95}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00268-y}, doi = {10.1007/S10822-019-00268-Y}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/MagantiB20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/MakarovM20, author = {G. I. Makarov and T. M. Makarova}, title = {A noncanonical binding site of linezolid revealed via molecular dynamics simulations}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {3}, pages = {281--291}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00269-x}, doi = {10.1007/S10822-019-00269-X}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/MakarovM20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/MecklenfeldR20, author = {Andreas Mecklenfeld and Gabriele Raabe}, title = {Applicability of a thermodynamic cycle approach for a force field parametrization targeting non-aqueous solvation free energies}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {1}, pages = {71--82}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00261-5}, doi = {10.1007/S10822-019-00261-5}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/MecklenfeldR20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/MiljkovicB20, author = {Filip Miljkovic and J{\"{u}}rgen Bajorath}, title = {Data structures for computational compound promiscuity analysis and exemplary applications to inhibitors of the human kinome}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {1}, pages = {1--10}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00266-0}, doi = {10.1007/S10822-019-00266-0}, timestamp = {Mon, 26 Oct 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/jcamd/MiljkovicB20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/MillsG20, author = {Alberto Mills and Federico Gago}, title = {Atomistic insight into sequence-directed {DNA} bending and minicircle formation propensity in the absence and presence of phased A-tracts}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {3}, pages = {253--265}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00288-z}, doi = {10.1007/S10822-020-00288-Z}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/MillsG20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/NguyenGWW20, author = {Duc Duy Nguyen and Kaifu Gao and Menglun Wang and Guo{-}Wei Wei}, title = {MathDL: mathematical deep learning for {D3R} Grand Challenge 4}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {2}, pages = {131--147}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00237-5}, doi = {10.1007/S10822-019-00237-5}, timestamp = {Mon, 01 Feb 2021 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/jcamd/NguyenGWW20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/NicolaKIA20, author = {George Nicola and Irina Kufareva and Andrey V. Ilatovskiy and Ruben Abagyan}, title = {Druggable exosites of the human kino-pocketome}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {3}, pages = {219--230}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00276-y}, doi = {10.1007/S10822-019-00276-Y}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/NicolaKIA20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/Nikitin20, author = {Alexei M. Nikitin}, title = {Non-zero Lennard-Jones parameters for the Toukan-Rahman water model: more accurate calculations of the solvation free energy of organic substances}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {4}, pages = {437--441}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00256-2}, doi = {10.1007/S10822-019-00256-2}, timestamp = {Thu, 27 May 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/Nikitin20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/OlandersABK20, author = {Gustav Olanders and Hiba Alogheli and Peter Brandt and Anders Karl{\'{e}}n}, title = {Conformational analysis of macrocycles: comparing general and specialized methods}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {3}, pages = {231--252}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00277-2}, doi = {10.1007/S10822-020-00277-2}, timestamp = {Fri, 14 May 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/OlandersABK20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/OlsonCCGJHALMK20, author = {Brian Olson and Anthony Cruz{-}Balberdy and Lieyang Chen and Mossa Ghattas and Yeonji Ji and Kunhui Huang and Steven Ayoub and Tyler Luchko and Daniel J. McKay and Tom Kurtzman}, title = {An online repository of solvation thermodynamic and structural maps of SARS-CoV-2 targets}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {12}, pages = {1219--1228}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00341-x}, doi = {10.1007/S10822-020-00341-X}, timestamp = {Thu, 16 Sep 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/OlsonCCGJHALMK20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/OuimetP20, author = {Jonathan A. Ouimet and Andrew S. Paluch}, title = {Predicting octanol/water partition coefficients for the {SAMPL6} challenge using the SM12, SM8, and {SMD} solvation models}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {5}, pages = {575--588}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00293-2}, doi = {10.1007/S10822-020-00293-2}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/OuimetP20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/PaciottiACS20, author = {Roberto Paciotti and Mariangela Agamennone and Cecilia Coletti and Loriano Storchi}, title = {Characterization of {PD-L1} binding sites by a combined {FMO/GRID-DRY} approach}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {8}, pages = {897--914}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00306-0}, doi = {10.1007/S10822-020-00306-0}, timestamp = {Mon, 03 Jan 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/jcamd/PaciottiACS20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/ParksGCYSWJMLBA20, author = {Conor D. Parks and Zied Gaieb and Michael Chiu and Huanwang Yang and Chenghua Shao and W. Patrick Walters and Johanna M. Jansen and Georgia B. McGaughey and Richard A. Lewis and Scott D. Bembenek and Michael K. Ameriks and Tara Mirzadegan and Stephen K. Burley and Rommie E. Amaro and Michael K. Gilson}, title = {{D3R} grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {2}, pages = {99--119}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00289-y}, doi = {10.1007/S10822-020-00289-Y}, timestamp = {Tue, 21 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/jcamd/ParksGCYSWJMLBA20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/PatelKJBW20, author = {Prajay Patel and David M. Kuntz and Michael R. Jones and Bernard R. Brooks and Angela K. Wilson}, title = {{SAMPL6} logP challenge: machine learning and quantum mechanical approaches}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {5}, pages = {495--510}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00287-0}, doi = {10.1007/S10822-020-00287-0}, timestamp = {Mon, 15 Jun 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/PatelKJBW20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/PathakDBCS20, author = {Bani Kumar Pathak and Debajyoti Das and Sayan Bhakta and Partha Chakrabarti and Jayati Sengupta}, title = {Resveratrol as a nontoxic excipient stabilizes insulin in a bioactive hexameric form}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {8}, pages = {915--927}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00311-3}, doi = {10.1007/S10822-020-00311-3}, timestamp = {Fri, 05 Nov 2021 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/jcamd/PathakDBCS20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/PeronaRMMG20, author = {Almudena Perona and M. Piedad Ros and Alberto Mills and Antonio Morreale and Federico Gago}, title = {Distinct binding of cetirizine enantiomers to human serum albumin and the human histamine receptor H\({}_{\mbox{1}}\)}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {10}, pages = {1045--1062}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00328-8}, doi = {10.1007/S10822-020-00328-8}, timestamp = {Sun, 11 Oct 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/PeronaRMMG20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/PrasadB20, author = {Samarjeet Prasad and Bernard R. Brooks}, title = {A deep learning approach for the blind logP prediction in {SAMPL6} challenge}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {5}, pages = {535--542}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00292-3}, doi = {10.1007/S10822-020-00292-3}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/PrasadB20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/Procacci20, author = {Piero Procacci}, title = {A remark on the efficiency of the double-system/single-box nonequilibrium approach in the {SAMPL6} SAMPLing challenge}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {6}, pages = {635--639}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00312-2}, doi = {10.1007/S10822-020-00312-2}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/Procacci20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/ProcacciG20, author = {Piero Procacci and Guido Guarnieri}, title = {{SAMPL6} blind predictions of water-octanol partition coefficients using nonequilibrium alchemical approaches}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {4}, pages = {371--384}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00233-9}, doi = {10.1007/S10822-019-00233-9}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/ProcacciG20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/RaczK20, author = {Anita R{\'{a}}cz and Gy{\"{o}}rgy M. Keser{\"{u}}}, title = {Large-scale evaluation of cytochrome {P450} 2C9 mediated drug interaction potential with machine learning-based consensus modeling}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {8}, pages = {831--839}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00308-y}, doi = {10.1007/S10822-020-00308-Y}, timestamp = {Fri, 14 May 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/RaczK20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/RajanR20, author = {Ravi Kumar Rajan and Muthiah Ramanathan}, title = {Identification and neuroprotective evaluation of a potential c-Jun N-terminal kinase 3 inhibitor through structure-based virtual screening and in-vitro assay}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {6}, pages = {671--682}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00297-y}, doi = {10.1007/S10822-020-00297-Y}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/RajanR20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/RedzepovicF20, author = {Izudin Redzepovic and Boris Furtula}, title = {Predictive potential of eigenvalue-based topological molecular descriptors}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {9}, pages = {975--982}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00320-2}, doi = {10.1007/S10822-020-00320-2}, timestamp = {Thu, 13 Aug 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/RedzepovicF20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/RiquelmeV20, author = {Maximiliano Riquelme and Esteban V{\"{o}}hringer{-}Martinez}, title = {{SAMPL6} Octanol-water partition coefficients from alchemical free energy calculations with {MBIS} atomic charges}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {4}, pages = {327--334}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00281-6}, doi = {10.1007/S10822-020-00281-6}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/RiquelmeV20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/RizziJSAGNBPHGC20, author = {Andrea Rizzi and Travis Jensen and David R. Slochower and Matteo Aldeghi and Vytautas Gapsys and Dimitris Ntekoumes and Stefano Bosisio and Michail Papadourakis and Niel M. Henriksen and Bert L. de Groot and Zoe Cournia and Alex Dickson and Julien Michel and Michael K. Gilson and Michael R. Shirts and David L. Mobley and John D. Chodera}, title = {The {SAMPL6} SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {5}, pages = {601--633}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00290-5}, doi = {10.1007/S10822-020-00290-5}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/RizziJSAGNBPHGC20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/RobinsonGL20, author = {Matthew C. Robinson and Robert C. Glen and Alpha A. Lee}, title = {Validating the validation: reanalyzing a large-scale comparison of deep learning and machine learning models for bioactivity prediction}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {7}, pages = {717--730}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00274-0}, doi = {10.1007/S10822-019-00274-0}, timestamp = {Fri, 14 May 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/RobinsonGL20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/Rodriguez-Perez20, author = {Raquel Rodr{\'{\i}}guez{-}P{\'{e}}rez and J{\"{u}}rgen Bajorath}, title = {Interpretation of machine learning models using shapley values: application to compound potency and multi-target activity predictions}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {10}, pages = {1013--1026}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00314-0}, doi = {10.1007/S10822-020-00314-0}, timestamp = {Fri, 14 May 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/Rodriguez-Perez20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/Sanchez-Marquez20, author = {Jes{\'{u}}s S{\'{a}}nchez{-}M{\'{a}}rquez and Victor Garc{\'{\i}}a and David Zorrilla and Manuel Fern{\'{a}}ndez}, title = {Software to obtain spatially localized functions from different radial functions}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {3}, pages = {267--280}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00272-2}, doi = {10.1007/S10822-019-00272-2}, timestamp = {Mon, 26 Oct 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/jcamd/Sanchez-Marquez20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/SarfarazML20, author = {Sara Sarfaraz and Iqra Muneer and Haiyan Liu}, title = {Combining fragment docking with graph theory to improve ligand docking for homology model structures}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {12}, pages = {1237--1259}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00345-7}, doi = {10.1007/S10822-020-00345-7}, timestamp = {Wed, 07 Dec 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/jcamd/SarfarazML20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/SasmalEM20, author = {Sukanya Sasmal and Lea El{-}Khoury and David L. Mobley}, title = {{D3R} Grand Challenge 4: ligand similarity and MM-GBSA-based pose prediction and affinity ranking for {BACE-1} inhibitors}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {2}, pages = {163--177}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00249-1}, doi = {10.1007/S10822-019-00249-1}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/SasmalEM20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/Sixto-LopezBC20, author = {Yudibeth Sixto{-}L{\'{o}}pez and Martiniano Bello and Jos{\'{e}} Correa{-}Basurto}, title = {Exploring the inhibitory activity of valproic acid against the {HDAC} family using an {MMGBSA} approach}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {8}, pages = {857--878}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00304-2}, doi = {10.1007/S10822-020-00304-2}, timestamp = {Mon, 26 Oct 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/jcamd/Sixto-LopezBC20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/SoniBJ20, author = {Anjali Soni and Ruchika Bhat and Bhyravabhotla Jayaram}, title = {Improving the binding affinity estimations of protein-ligand complexes using machine-learning facilitated force field method}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {8}, pages = {817--830}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00305-1}, doi = {10.1007/S10822-020-00305-1}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/SoniBJ20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/StroganovNMDGSC20, author = {Oleg V. Stroganov and Fedor N. Novikov and Michael G. Medvedev and Artem O. Dmitrienko and Igor S. Gerasimov and Igor V. Svitanko and Ghermes G. Chilov}, title = {The role of human in the loop: lessons from {D3R} challenge 4}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {2}, pages = {121--130}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00291-4}, doi = {10.1007/S10822-020-00291-4}, timestamp = {Wed, 06 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/jcamd/StroganovNMDGSC20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/StumpfeHB20, author = {Dagmar Stumpfe and Huabin Hu and J{\"{u}}rgen Bajorath}, title = {Advances in exploring activity cliffs}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {9}, pages = {929--942}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00315-z}, doi = {10.1007/S10822-020-00315-Z}, timestamp = {Fri, 14 May 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/StumpfeHB20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/SunHLZ20, author = {Zhaoxi Sun and Qiao{-}Le He and Xiao Li and Zhengdan Zhu}, title = {{SAMPL6} host-guest binding affinities and binding poses from spherical-coordinates-biased simulations}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {5}, pages = {589--600}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00294-1}, doi = {10.1007/S10822-020-00294-1}, timestamp = {Thu, 23 Jun 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/SunHLZ20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/SzwabowskiCSWCB20, author = {Gregory L. Szwabowski and Paige N. Castleman and Chandler K. Sears and Lee H. Wink and Judith A. Cole and Daniel L. Baker and Abby L. Parrill}, title = {Benchmarking {GPCR} homology model template selection in combination with de novo loop generation}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {10}, pages = {1027--1044}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00325-x}, doi = {10.1007/S10822-020-00325-X}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/SzwabowskiCSWCB20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/Thiruchittampalam20, author = {Shalini Thiruchittampalam and Samantha Weerasinghe}, title = {Plausible compounds drawn from plants as curative agents for neurodegeneration: An in-silico approach}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {9}, pages = {1003--1011}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00322-0}, doi = {10.1007/S10822-020-00322-0}, timestamp = {Thu, 14 Oct 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/Thiruchittampalam20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/TielkerTEGK20, author = {Nicolas Tielker and Daniel Tomazic and Lukas Eberlein and Stefan G{\"{u}}ssregen and Stefan M. Kast}, title = {The {SAMPL6} challenge on predicting octanol-water partition coefficients from {EC-RISM} theory}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {4}, pages = {453--461}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00283-4}, doi = {10.1007/S10822-020-00283-4}, timestamp = {Fri, 14 May 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/TielkerTEGK20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/TikhonovLYYZ20, author = {Denis B. Tikhonov and Lianyun Lin and Daniel S. C. Yang and Zhiguang Yuchi and Boris S. Zhorov}, title = {Phenylalkylamines in calcium channels: computational analysis of experimental structures}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {11}, pages = {1157--1169}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00330-0}, doi = {10.1007/S10822-020-00330-0}, timestamp = {Tue, 20 Oct 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/TikhonovLYYZ20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/TripathiSTTSSS20, author = {Manish Kumar Tripathi and Piyoosh Sharma and Avanish Tripathi and Prabhash Nath Tripathi and Pavan Srivastava and Ankit Seth and Sushant Kumar Shrivastava}, title = {Computational exploration and experimental validation to identify a dual inhibitor of cholinesterase and amyloid-beta for the treatment of Alzheimer's disease}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {9}, pages = {983--1002}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00318-w}, doi = {10.1007/S10822-020-00318-W}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/TripathiSTTSSS20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/VangalaSPM20, author = {Radhika Vangala and Sree Kanth Sivan and Saikiran Reddy Peddi and Vijjulatha Manga}, title = {Computational design, synthesis and evaluation of new sulphonamide derivatives targeting {HIV-1} gp120}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {1}, pages = {39--54}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00258-0}, doi = {10.1007/S10822-019-00258-0}, timestamp = {Mon, 26 Oct 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/jcamd/VangalaSPM20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/WangN20, author = {Bo Wang and Ho{-}Leung Ng}, title = {Deep neural network affinity model for {BACE} inhibitors in {D3R} Grand Challenge 4}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {2}, pages = {201--217}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00275-z}, doi = {10.1007/S10822-019-00275-Z}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/WangN20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/WangR20, author = {Shuzhe Wang and Sereina Riniker}, title = {Use of molecular dynamics fingerprints (MDFPs) in {SAMPL6} octanol-water log {P} blind challenge}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {4}, pages = {393--403}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00252-6}, doi = {10.1007/S10822-019-00252-6}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/WangR20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/WangRZ20, author = {Huiqun Wang and Bethany A. Reinecke and Yan Zhang}, title = {Computational insights into the molecular mechanisms of differentiated allosteric modulation at the mu opioid receptor by structurally similar bitopic modulators}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {8}, pages = {879--895}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00309-x}, doi = {10.1007/S10822-020-00309-X}, timestamp = {Tue, 13 Oct 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/WangRZ20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/WebelKRNNV20, author = {Henry E. Webel and Talia B. Kimber and Silke Radetzki and Martin Neuenschwander and Marc Nazar{\'{e}} and Andrea Volkamer}, title = {Revealing cytotoxic substructures in molecules using deep learning}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {7}, pages = {731--746}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00310-4}, doi = {10.1007/S10822-020-00310-4}, timestamp = {Fri, 14 May 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/WebelKRNNV20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/XiaKPT20, author = {Zhonghua Xia and Pavel Karpov and Grzegorz M. Popowicz and Igor V. Tetko}, title = {Focused Library Generator: case of Mdmx inhibitors}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {7}, pages = {769--782}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00242-8}, doi = {10.1007/S10822-019-00242-8}, timestamp = {Wed, 15 Jun 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/XiaKPT20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/XuZCLSRLZC20, author = {Xiaoqian Xu and Li Zhang and Ying Cai and Dongxin Liu and Zhengwen Shang and Qiuhong Ren and Qiong Li and Weidong Zhao and Yuhua Chen}, title = {Inhibitor discovery for the E. coli meningitis virulence factor IbeA from homology modeling and virtual screening}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {1}, pages = {11--25}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00250-8}, doi = {10.1007/S10822-019-00250-8}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/XuZCLSRLZC20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/YauEL20, author = {Mei Qian Yau and Abigail L. Emtage and Jason S. E. Loo}, title = {Benchmarking the performance of {MM/PBSA} in virtual screening enrichment using the GPCR-Bench dataset}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {11}, pages = {1133--1145}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00339-5}, doi = {10.1007/S10822-020-00339-5}, timestamp = {Mon, 03 Jan 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/jcamd/YauEL20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/YazarO20, author = {Metin Yazar and Pemra Ozbek}, title = {Revisiting allostery in CREB-binding protein {(CBP)} using residue-based interaction energy}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {9}, pages = {965--974}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00316-y}, doi = {10.1007/S10822-020-00316-Y}, timestamp = {Thu, 13 Aug 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/YazarO20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/YonchevB20, author = {Dimitar G. Yonchev and J{\"{u}}rgen Bajorath}, title = {DeepCOMO: from structure-activity relationship diagnostics to generative molecular design using the compound optimization monitor methodology}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {12}, pages = {1207--1218}, year = {2020}, url = {https://doi.org/10.1007/s10822-020-00349-3}, doi = {10.1007/S10822-020-00349-3}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/YonchevB20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/ZamoraPGRCL20, author = {William J. Zamora and Silvana Pinheiro and Kilian German and Clara P{\'{e}}rez{-}R{\`{a}}fols and Carles Curutchet and F. Javier Luque}, title = {Prediction of the n-octanol/water partition coefficients in the {SAMPL6} blind challenge from {MST} continuum solvation calculations}, journal = {J. Comput. Aided Mol. Des.}, volume = {34}, number = {4}, pages = {443--451}, year = {2020}, url = {https://doi.org/10.1007/s10822-019-00262-4}, doi = {10.1007/S10822-019-00262-4}, timestamp = {Mon, 25 Apr 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/ZamoraPGRCL20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
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