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ORCIDJournal of Computer-Aided Molecular Design, Volume 38
Volume 38, Number 1, December 2024
- Adan Gallardo, Bercem Dutagaci
:
Binding of small molecule inhibitors to RNA polymerase-Spt5 complex impacts RNA and DNA stability. 1 - Liliana Halip, Sorin I. Avram, Ramona Curpan, Ana Borota, Alina Bora, Cristian Bologa, Tudor I. Oprea:
Correction: Exploring DrugCentral: from molecular structures to clinical effects. 2 - Andrew T. McNutt, David Ryan Koes:
Open-ComBind: harnessing unlabeled data for improved binding pose prediction. 3 - Patrick Penner, Anna Vulpetti:
QM assisted ML for 19F NMR chemical shift prediction. 4 - Aleksei Kabedev, Christel A. S. Bergström, Per Larsson:
Molecular dynamics study on micelle-small molecule interactions: developing a strategy for an extensive comparison. 5 - Maria Lazou, Jonathan R. Hutton, Arijit Chakravarty, Diane Joseph-McCarthy:
Identification of a druggable site on GRP78 at the GRP78-SARS-CoV-2 interface and virtual screening of compounds to disrupt that interface. 6 - Florian Führer, Andrea Gruber, Holger Diedam, Andreas H. Göller, Stephan Menz, Sebastian Schneckener:
A deep neural network: mechanistic hybrid model to predict pharmacokinetics in rat. 7 - Md Fulbabu Sk, Sunanda Samanta, Sayan Poddar, Parimal Kar:
Deciphering the molecular choreography of Janus kinase 2 inhibition via Gaussian accelerated molecular dynamics simulations: a dynamic odyssey. 8 - José Ramón Mora, Edgar Márquez, Noel Pérez-Pérez, Ernesto Contreras-Torres, Yunierkis Pérez-Castillo, Guillermín Agüero-Chapín, Felix Martinez-Rios, Yovani Marrero-Ponce, Stephen J. Barigye:
Rethinking the applicability domain analysis in QSAR models. 9 - Azam Nesabi, Jas Kalayan, Sara Al Rawashdeh, Mohammad A. Ghattas, Richard A. Bryce:
Molecular dynamics simulations as a guide for modulating small molecule aggregation. 11 - Ajay N. Jain, Alexander C. Brueckner, Christine Jorge, Ann E. Cleves, Purnima Khandelwal, Janet Caceres Cortes, Luciano Mueller:
Correction: Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design. 12 - Sophia M. N. Hönig, Florian Flachsenberg, Christiane Ehrt, Alexander Neumann, Robert Schmidt, Christian Lemmen, Matthias Rarey:
SpaceGrow: efficient shape-based virtual screening of billion-sized combinatorial fragment spaces. 13 - Jeremy Jones, Robert D. Clark, Michael S. Lawless, David W. Miller, Marvin Waldman:
The AI-driven Drug Design (AIDD) platform: an interactive multi-parameter optimization system integrating molecular evolution with physiologically based pharmacokinetic simulations. 14 - Irem N. Zengin, M. Serdar Koca, Omer Tayfuroglu, Muslum Yildiz, Abdulkadir Kocak:
Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 Mpro. 15 - Samia A. Elseginy:
Identifying and characterising promising small molecule inhibitors of kinesin spindle protein using ligand-based virtual screening, molecular docking, molecular dynamics and MM‑GBSA calculations. 16 - Nicolas Scalzitti, Iliya Miralavy, David E. Korenchan, Christian T. Farrar, Assaf A. Gilad, Wolfgang Banzhaf:
Computational peptide discovery with a genetic programming approach. 17 - Javier Vázquez, Ricardo García, Paula Llinares, F. Javier Luque, Enric Herrero:
On the relevance of query definition in the performance of 3D ligand-based virtual screening. 18 - Ann E. Cleves, Ajay N. Jain, David A. Demeter, Zachary A. Buchan, Jeremy Wilmot, Erin N. Hancock:
From UK-2A to florylpicoxamid: Active learning to identify a mimic of a macrocyclic natural product. 19 - Gavin Ye:
De novo drug design as GPT language modeling: large chemistry models with supervised and reinforcement learning. 20 - Aaron D. Danilack, Callum J. Dickson, Cihan Soylu, Mike Fortunato, Stephane Rodde, Hagen Münkler, Viktor Hornak, José S. Duca:
Reactivities of acrylamide warheads toward cysteine targets: a QM/ML approach to covalent inhibitor design. 21 - Robert X. Song, Marc C. Nicklaus, Nadya I. Tarasova:
Correlation of protein binding pocket properties with hits' chemistries used in generation of ultra-large virtual libraries. 22 - Konrad Diedrich, Christiane Ehrt, Joel Graef, Martin Poppinga, Norbert Ritter, Matthias Rarey:
User-centric design of a 3D search interface for protein-ligand complexes. 23 - Alexander C. Brueckner, Benjamin Shields, Palani Kirubakaran, Alexander Suponya, Manoranjan Panda, Shana L. Posy, Stephen R. Johnson, Sirish Kaushik Lakkaraju:
MDFit: automated molecular simulations workflow enables high throughput assessment of ligands-protein dynamics. 24 - Wen-Chieh Huang, Chia-Hung Hsu, Titus V. Albu, Chia-Ning Yang:
Structural impacts of two disease-linked ADAR1 mutants: a molecular dynamics study. 25 - Laura Guasch, Niels Maeder, John G. Cumming, Christian Kramer:
From mundane to surprising nonadditivity: drivers and impact on ML models. 26 - Lucas A. Garro, Matias F. Andrada, Esteban G. Vega-Hissi, Sonia Barberis, Juan C. Garro Martinez:
Development of QSARs for cysteine-containing di- and tripeptides with antioxidant activity:influence of the cysteine position. 27 - Yuanyuan Shu, Jianda Yue, Yaqi Li, Yekui Yin, Jiaxu Wang, Tingting Li, Xiao He, Songping Liang, Gaihua Zhang, Zhonghua Liu, Ying Wang:
Development of human lactate dehydrogenase a inhibitors: high-throughput screening, molecular dynamics simulation and enzyme activity assay. 28 - Daniel K. Gehlhaar, Daniel J. Mermelstein:
FitScore: a fast machine learning-based score for 3D virtual screening enrichment. 29 - Daniel A. M. Pais, Jan-Peter A. Mayer, Karin Felderer, Maria B. Batalha, Timo Eichner, Sofia T. Santos, Raman Kumar, Sandra D. Silva, Hitto Kaufmann:
Holistic in silico developability assessment of novel classes of small proteins using publicly available sequence-based predictors. 30 - Kaipeng Li, Lijun Liu:
Computational design and experimental confirmation of a disulfide-stapled YAP helixα1-trap derived from TEAD4 helical hairpin to selectively capture YAP α1-helix with potent antitumor activity. 31 - Hyosoon Jang, Sangmin Seo, Sanghyun Park, Byung Ju Kim, Geon-Woo Choi, Jonghwan Choi, Chihyun Park:
De novo drug design through gradient-based regularized search in information-theoretically controlled latent space. 32 - Ann E. Cleves, Himani Tandon, Ajay N. Jain:
Structure-based pose prediction: Non-cognate docking extended to macrocyclic ligands. 33 - Phuc-Chau Do, Vy T. T. Le:
Steered molecular dynamics simulation as a post-process to optimize the iBRAB-designed Fab model. 34 - Tugay Direk, Osman Doluca:
Computational Identification and Illustrative Standard for Representation of Unimolecular G-Quadruplex Secondary Structures (CIIS-GQ). 35 - Adiran Garaizar Suarez, Andreas H. Göller, Michael E. Beck, Sadra Kashef Ol Gheta, Katharina Meier:
Comparative assessment of physics-based in silico methods to calculate relative solubilities. 36 - Hui Zhang, Hua-Zhao Qi, Ya-Juan Li, Xiu-Yun Shi, Mei-Ling Hu, Xiang-Long Chen, Yuan Li:
Identification of novel inhibitors targeting PI3Kα via ensemble-based virtual screening method, biological evaluation and molecular dynamics simulation. 37 - Monika Phougat, Narinder Singh Sahni, Devapriya Choudhury:
Understanding the relationship between preferential interactions of peptides in water-acetonitrile mixtures with protein-solvent contact surface area. 38
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