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@article{DBLP:journals/jcisd/CaseABCCCFGGGIKKKKLLLLLMMNOOPPQRR23,
  author       = {David A. Case and
                  Hasan Metin Aktulga and
                  Kellon Belfon and
                  David S. Cerutti and
                  G. Andr{\'{e}}s Cisneros and
                  Vin{\'{\i}}cius Wilian D. Cruzeiro and
                  Negin Forouzesh and
                  Timothy J. Giese and
                  Andreas W. G{\"{o}}tz and
                  Holger Gohlke and
                  Saeed Izadi and
                  Koushik Kasavajhala and
                  Mehmet Cagri Kaymak and
                  Edward King and
                  Tom Kurtzman and
                  Tai{-}Sung Lee and
                  Pengfei Li and
                  Jian Liu and
                  Tyler Luchko and
                  Ray Luo and
                  Madushanka Manathunga and
                  Mat{\'{\i}}as R. Machado and
                  Hai Minh Nguyen and
                  Kurt A. O'Hearn and
                  Alexey V. Onufriev and
                  Feng Pan and
                  Sergio Pantano and
                  Ruxi Qi and
                  Ali Rahnamoun and
                  Ali Risheh and
                  Stephan Schott{-}Verdugo and
                  Akhil Shajan and
                  Jason M. Swails and
                  Junmei Wang and
                  Haixin Wei and
                  Xiongwu Wu and
                  Yongxian Wu and
                  Shi Zhang and
                  Shiji Zhao and
                  Qiang Zhu and
                  Thomas E. Cheatham and
                  Daniel R. Roe and
                  Adrian E. Roitberg and
                  Carlos Simmerling and
                  Darrin M. York and
                  Maria C. Nagan and
                  Kenneth M. Merz Jr.},
  title        = {AmberTools},
  journal      = {J. Chem. Inf. Model.},
  volume       = {63},
  number       = {20},
  pages        = {6183--6191},
  year         = {2023},
  url          = {https://doi.org/10.1021/acs.jcim.3c01153},
  doi          = {10.1021/ACS.JCIM.3C01153},
  timestamp    = {Mon, 05 Feb 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/jcisd/CaseABCCCFGGGIKKKKLLLLLMMNOOPPQRR23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcisd/StepanenkoBS23,
  author       = {Darya Stepanenko and
                  Stephanie Budhan and
                  Carlos Simmerling},
  title        = {SpikeScape: {A} Tool for Analyzing Structural Diversity in Experimental
                  Structures of the SARS-CoV-2 Spike Glycoprotein},
  journal      = {J. Chem. Inf. Model.},
  volume       = {63},
  number       = {4},
  pages        = {1087--1092},
  year         = {2023},
  url          = {https://doi.org/10.1021/acs.jcim.2c01366},
  doi          = {10.1021/ACS.JCIM.2C01366},
  timestamp    = {Tue, 21 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/jcisd/StepanenkoBS23.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ijhpca/CasalinoDGBSATB21,
  author       = {Lorenzo Casalino and
                  Abigail C. Dommer and
                  Zied Gaieb and
                  Em{\'{\i}}lia P. Barros and
                  Terra Sztain and
                  Surl{-}Hee Ahn and
                  Anda Trifan and
                  Alexander Brace and
                  Anthony T. Bogetti and
                  Austin Clyde and
                  Heng Ma and
                  Hyungro Lee and
                  Matteo Turilli and
                  Syma Khalid and
                  Lillian T. Chong and
                  Carlos Simmerling and
                  David J. Hardy and
                  Julio D. C. Maia and
                  James C. Phillips and
                  Thorsten Kurth and
                  Abraham C. Stern and
                  Lei Huang and
                  John D. McCalpin and
                  Mahidhar Tatineni and
                  Tom Gibbs and
                  John E. Stone and
                  Shantenu Jha and
                  Arvind Ramanathan and
                  Rommie E. Amaro},
  title        = {AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2
                  spike dynamics},
  journal      = {Int. J. High Perform. Comput. Appl.},
  volume       = {35},
  number       = {5},
  year         = {2021},
  url          = {https://doi.org/10.1177/10943420211006452},
  doi          = {10.1177/10943420211006452},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ijhpca/CasalinoDGBSATB21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcamd/ZouTS19,
  author       = {Junjie Zou and
                  Chuan Tian and
                  Carlos Simmerling},
  title        = {Blinded prediction of protein-ligand binding affinity using Amber
                  thermodynamic integration for the 2018 {D3R} grand challenge 4},
  journal      = {J. Comput. Aided Mol. Des.},
  volume       = {33},
  number       = {12},
  pages        = {1021--1029},
  year         = {2019},
  url          = {https://doi.org/10.1007/s10822-019-00223-x},
  doi          = {10.1007/S10822-019-00223-X},
  timestamp    = {Thu, 14 Oct 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcamd/ZouTS19.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ijcga/HummelYSC18,
  author       = {Michelle Hatch Hummel and
                  Bihua Yu and
                  Carlos Simmerling and
                  Evangelos A. Coutsias},
  title        = {Laguerre-Intersection Method for Implicit Solvation},
  journal      = {Int. J. Comput. Geom. Appl.},
  volume       = {28},
  number       = {1},
  pages        = {1--38},
  year         = {2018},
  url          = {https://doi.org/10.1142/S0218195918500012},
  doi          = {10.1142/S0218195918500012},
  timestamp    = {Thu, 04 Jun 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ijcga/HummelYSC18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcisd/HauserHGSC17,
  author       = {Kevin Hauser and
                  Yiqing He and
                  Miguel Garcia{-}Diaz and
                  Carlos Simmerling and
                  Evangelos A. Coutsias},
  title        = {Characterization of Biomolecular Helices and Their Complementarity
                  Using Geometric Analysis},
  journal      = {J. Chem. Inf. Model.},
  volume       = {57},
  number       = {4},
  pages        = {864--874},
  year         = {2017},
  url          = {https://doi.org/10.1021/acs.jcim.6b00721},
  doi          = {10.1021/ACS.JCIM.6B00721},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcisd/HauserHGSC17.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/corr/abs-1712-06956,
  author       = {Michelle Hatch Hummel and
                  Bihua Yu and
                  Carlos Simmerling and
                  Evangelos A. Coutsias},
  title        = {Laguerre-Intersection Method for Implicit Solvation},
  journal      = {CoRR},
  volume       = {abs/1712.06956},
  year         = {2017},
  url          = {http://arxiv.org/abs/1712.06956},
  eprinttype    = {arXiv},
  eprint       = {1712.06956},
  timestamp    = {Mon, 13 Aug 2018 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/corr/abs-1712-06956.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcc/SongHSGS08,
  author       = {Kun Song and
                  Viktor Hornak and
                  Carlos De Los Santos and
                  Arthur P. Grollman and
                  Carlos Simmerling},
  title        = {Molecular mechanics parameters for the FapydG {DNA} lesion},
  journal      = {J. Comput. Chem.},
  volume       = {29},
  number       = {1},
  pages        = {17--23},
  year         = {2008},
  url          = {https://doi.org/10.1002/jcc.20625},
  doi          = {10.1002/JCC.20625},
  timestamp    = {Wed, 01 Apr 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcc/SongHSGS08.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcc/CaseCDGLMOSWW05,
  author       = {David A. Case and
                  Thomas E. Cheatham III and
                  Tom Darden and
                  Holger Gohlke and
                  Ray Luo and
                  Kenneth M. Merz Jr. and
                  Alexey Onufriev and
                  Carlos Simmerling and
                  Bing Wang and
                  Robert J. Woods},
  title        = {The Amber biomolecular simulation programs},
  journal      = {J. Comput. Chem.},
  volume       = {26},
  number       = {16},
  pages        = {1668--1688},
  year         = {2005},
  url          = {https://doi.org/10.1002/jcc.20290},
  doi          = {10.1002/JCC.20290},
  timestamp    = {Mon, 24 Apr 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcc/CaseCDGLMOSWW05.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcc/OkurSHS03,
  author       = {Asim Okur and
                  Bentley Strockbine and
                  Viktor Hornak and
                  Carlos Simmerling},
  title        = {Using {PC} clusters to evaluate the transferability of molecular mechanics
                  force fields for proteins},
  journal      = {J. Comput. Chem.},
  volume       = {24},
  number       = {1},
  pages        = {21--31},
  year         = {2003},
  url          = {https://doi.org/10.1002/jcc.10184},
  doi          = {10.1002/JCC.10184},
  timestamp    = {Wed, 01 Apr 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcc/OkurSHS03.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
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