The inclusion of electrostatic hydration energies in molecular mechanics calculations. - Michael K. Gilson; Barry Honig (J. Comput. Aided Mol. Des., 1991)

Computing ionization states of proteins with a detailed charge model. - Jan Antosiewicz; James M. Briggs; Adrian H. Elcock; Michael K. Gilson; James Andrew McCammon (J. Comput. Chem., 1996)

Comparison of generalized born and poisson models: Energetics and dynamics of HIV protease. - Laurent David; Ray Luo 001; Michael K. Gilson (J. Comput. Chem., 2000)

Ligand-receptor docking with the Mining Minima optimizer. - Laurent David; Ray Luo 001; Michael K. Gilson (J. Comput. Aided Mol. Des., 2001)

The Binding Database: data management and interface design. - Xi Chen; Yuhmei Lin; Ming Liu; Michael K. Gilson (Bioinform., 2002)

Enhanced docking with the mining minima optimizer: Acceleration and side-chain flexibility. - Visvaldas Kairys; Michael K. Gilson (J. Comput. Chem., 2002)

Accelerated Poisson-Boltzmann calculations for static and dynamic systems. - Ray Luo 001; Laurent David; Michael K. Gilson (J. Comput. Chem., 2002)

Tork: Conformational analysis method for molecules and complexes. - Chia-En Chang; Michael K. Gilson (J. Comput. Chem., 2003)

Fast Assignment of Accurate Partial Atomic Charges: An Electronegativity Equalization Method that Accounts for Alternate Resonance Forms. - Michael K. Gilson; Hillary S. R. Gilson; Michael J. Potter (J. Chem. Inf. Comput. Sci., 2003)

ASAP, a systematic annotation package for community analysis of genomes. - Jeremy D. Glasner; Paul Liss; Guy Plunkett III; Aaron E. Darling; Tejasvini Prasad; Michael Rusch; Alexis Byrnes; Michael K. Gilson; Bryan S. Biehl; Frederick R. Blattner; Nicole T. Perna (Nucleic Acids Res., 2003)

Identification of Symmetries in Molecules and Complexes. - Wei Chen; Jing Huang; Michael K. Gilson (J. Chem. Inf. Model., 2004)

Comparing Ligand Interactions with Multiple Receptors via Serial Docking. - Miguel X. Fernandes; Visvaldas Kairys; Michael K. Gilson (J. Chem. Inf. Model., 2004)

Virtual Screening of Molecular Databases Using a Support Vector Machine. - Robert N. Jorissen; Michael K. Gilson (J. Chem. Inf. Model., 2005)

Screening Drug-Like Compounds by Docking to Homology Models: A Systematic Study. - Visvaldas Kairys; Miguel X. Fernandes; Michael K. Gilson (J. Chem. Inf. Model., 2006)

ConCept: de Novo Design of Synthetic Receptors for Targeted Ligands. - Wei Chen; Michael K. Gilson (J. Chem. Inf. Model., 2007)

ConCept: de Novo Design of Synthetic Receptors for Targeted Ligands [J. Chem. Inf. Model, 47, 425-434 (2007)]. - Wei Chen; Michael K. Gilson (J. Chem. Inf. Model., 2007)

BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. - Tiqing Liu; Yuhmei Lin; Xin Wen; Robert N. Jorissen; Michael K. Gilson (Nucleic Acids Res., 2007)

Efficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methods. - Vladimir Hnizdo; Jun Tan; Benjamin J. Killian; Michael K. Gilson (J. Comput. Chem., 2008)

Thermodynamic and Differential Entropy under a Change of Variables. - Vladimir Hnizdo; Michael K. Gilson (Entropy, 2010)

Prediction of SAMPL3 host-guest binding affinities: evaluating the accuracy of generalized force-fields. - Hari S. Muddana; Michael K. Gilson (J. Comput. Aided Mol. Des., 2012)

Blind prediction of host-guest binding affinities: a new SAMPL3 challenge. - Hari S. Muddana; C. Daniel Varnado; Christopher W. Bielawski; Adam R. Urbach; Lyle Isaacs; Matthew T. Geballe; Michael K. Gilson (J. Comput. Aided Mol. Des., 2012)

SuperTarget goes quantitative: update on drug-target interactions. - Nikolai Hecker; Jessica Ahmed; Joachim von Eichborn; Mathias Dunkel; Karel Macha; Andreas Eckert; Michael K. Gilson; Philip E. Bourne; Robert Preissner (Nucleic Acids Res., 2012)

Overcoming dissipation in the calculation of standard binding free energies by ligand extraction. - Camilo Velez-Vega; Michael K. Gilson (J. Comput. Chem., 2013)

The SAMPL4 host-guest blind prediction challenge: an overview. - Hari S. Muddana; Andrew T. Fenley; David L. Mobley; Michael K. Gilson (J. Comput. Aided Mol. Des., 2014)

The SAMPL4 hydration challenge: evaluation of partial charge sets with explicit-water molecular dynamics simulations. - Hari S. Muddana; Neil V. Sapra; Andrew T. Fenley; Michael K. Gilson (J. Comput. Aided Mol. Des., 2014)

Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method. - Hari S. Muddana; Jian Yin 005; Neil V. Sapra; Andrew T. Fenley; Michael K. Gilson (J. Comput. Aided Mol. Des., 2014)

Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME. - George Nicola; Michael R. Berthold; Michael P. Hedrick; Michael K. Gilson (Database J. Biol. Databases Curation, 2015)

Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge. - Caitlin C. Bannan; Kalistyn H. Burley; Michael Chiu; Michael R. Shirts; Michael K. Gilson; David L. Mobley (J. Comput. Aided Mol. Des., 2016)

D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions. - Symon Gathiaka; Shuai Liu; Michael Chiu; Huanwang Yang; Jeanne A. Stuckey; You-Na Kang; Jim Delproposto; Ginger Kubish; James B. Dunbar Jr.; Heather A. Carlson; Stephen K. Burley; W. Patrick Walters; et al. (J. Comput. Aided Mol. Des., 2016)

Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST. - Steven Ramsey; Crystal Nguyen; Romelia Salomón-Ferrer; Ross C. Walker; Michael K. Gilson; Tom Kurtzman (J. Comput. Chem., 2016)

BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology. - Michael K. Gilson; Tiqing Liu; Michael Baitaluk; George Nicola; Linda Hwang; Jenny Chong (Nucleic Acids Res., 2016)

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. - Michael R. Shirts; Christoph Klein 003; Jason M. Swails; Jian Yin 005; Michael K. Gilson; David L. Mobley; David A. Case; Ellen D. Zhong (J. Comput. Aided Mol. Des., 2017)

Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. - Michael R. Shirts; Christoph Klein 003; Jason M. Swails; Jian Yin 005; Michael K. Gilson; David L. Mobley; David A. Case; Ellen D. Zhong (J. Comput. Aided Mol. Des., 2017)

The SAMPL5 host-guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method. - Jian Yin 005; Niel M. Henriksen; David R. Slochower; Michael K. Gilson (J. Comput. Aided Mol. Des., 2017)

Overview adcm43.bhtof the SAMPL5 host-guest challenge: Are we doing better? - Jian Yin 005; Niel M. Henriksen; David R. Slochower; Michael R. Shirts; Michael Chiu; David L. Mobley; Michael K. Gilson (J. Comput. Aided Mol. Des., 2017)

D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. - Zied Gaieb; Shuai Liu; Symon Gathiaka; Michael Chiu; Huanwang Yang; Chenghua Shao; Victoria A. Feher; W. Patrick Walters; Bernd Kuhn; Markus G. Rudolph; Stephen K. Burley; Michael K. Gilson; et al. (J. Comput. Aided Mol. Des., 2018)

Overview of the SAMPL6 host-guest binding affinity prediction challenge. - Andrea Rizzi; Steven Murkli; John N. McNeill; Wei Yao 010; Matthew R. Sullivan; Michael K. Gilson; Michael Chiu; Lyle Isaacs; Bruce C. Gibb; David L. Mobley; John D. Chodera (J. Comput. Aided Mol. Des., 2018)

D3R Grand Challenge 3: blind prediction of protein-ligand poses and affinity rankings. - Zied Gaieb; Conor D. Parks; Michael Chiu; Huanwang Yang; Chenghua Shao; W. Patrick Walters; Millard H. Lambert; Neysa Nevins; Scott D. Bembenek; Michael K. Ameriks; Tara Mirzadegan; Stephen K. Burley; et al. (J. Comput. Aided Mol. Des., 2019)

This issue: Drug Design Data Resource Grand Challenge 4, first of two issues. - Michael K. Gilson (J. Comput. Aided Mol. Des., 2019)

Drug Design Data Resource, Grand Challenge 4, second of two issues. - Michael K. Gilson; Rommie E. Amaro (J. Comput. Aided Mol. Des., 2020)

D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. - Conor D. Parks; Zied Gaieb; Michael Chiu; Huanwang Yang; Chenghua Shao; W. Patrick Walters; Johanna M. Jansen; Georgia B. McGaughey; Richard A. Lewis; Scott D. Bembenek; Michael K. Ameriks; Tara Mirzadegan; et al. (J. Comput. Aided Mol. Des., 2020)

The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. - Andrea Rizzi; Travis Jensen; David R. Slochower; Matteo Aldeghi; Vytautas Gapsys; Dimitris Ntekoumes; Stefano Bosisio; Michail Papadourakis; Niel M. Henriksen; Bert L. de Groot; Zoe Cournia; Alex Dickson; et al. (J. Comput. Aided Mol. Des., 2020)

Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo. - Teresa Danielle Bergazin; Ido Y. Ben-Shalom; Nathan M. Lim; Sam C. Gill; Michael K. Gilson; David L. Mobley (J. Comput. Aided Mol. Des., 2021)

Experimental characterization of the association of β-cyclodextrin and eight novel cyclodextrin derivatives with two guest compounds. - K. Kellett; David R. Slochower; Michael Schauperl; B. M. Duggan; Michael K. Gilson (J. Comput. Aided Mol. Des., 2021)

Alignment-Free Antimicrobial Peptide Predictors: Improving Performance by a Thorough Analysis of the Largest Available Data Set. - Sergio Alejandro Pinacho-Castellanos; César R. García-Jacas; Michael K. Gilson; Carlos A. Brizuela (J. Chem. Inf. Model., 2021)

Correction to Alignment-Free Antimicrobial Peptide Predictors: Improving Performance by a Thorough Analysis of the Largest Available Data Set. - Sergio Alejandro Pinacho-Castellanos; César R. García-Jacas; Michael K. Gilson; Carlos A. Brizuela (J. Chem. Inf. Model., 2021)

Improving Structure-Based Virtual Screening with Ensemble Docking and Machine Learning. - Joel Ricci-Lopez; Sergio A. Aguila; Michael K. Gilson; Carlos A. Brizuela (J. Chem. Inf. Model., 2021)

LIMO: Latent Inceptionism for Targeted Molecule Generation. - Peter Eckmann; Kunyang Sun; Bo Zhao 028; Mudong Feng; Michael K. Gilson; Rose Yu (ICML, 2022)

Target-Free Compound Activity Prediction via Few-Shot Learning. - Peter Eckmann; Jake Anderson; Michael K. Gilson; Rose Yu (CoRR, 2023)

MFBind: a Multi-Fidelity Approach for Evaluating Drug Compounds in Practical Generative Modeling. - Peter Eckmann; Dongxia Wu; Germano Heinzelmann; Michael K. Gilson; Rose Yu (CoRR, 2024)

Technical report: Improving the properties of molecules generated by LIMO. - Vineet Thumuluri; Peter Eckmann; Michael K. Gilson; Rose Yu (CoRR, 2024)

MF-LAL: Drug Compound Generation Using Multi-Fidelity Latent Space Active Learning. - Peter Eckmann; Dongxia Wu; Germano Heinzelmann; Michael K. Gilson; Rose Yu (CoRR, 2024)

Ligand-Based Compound Activity Prediction via Few-Shot Learning. - Peter Eckmann; Jake Anderson; Rose Yu; Michael K. Gilson (J. Chem. Inf. Model., 2024)

The Need for Continuing Blinded Pose- and Activity Prediction Benchmarks. - Christian Kramer; John D. Chodera; Kelly L. Damm-Ganamet; Michael K. Gilson; Judith Guenther; Uta F. Lessel; Richard A. Lewis; David L. Mobley; Eva Nittinger; Adam Pecina; Matthieu Schapira; W. Patrick Walters (J. Chem. Inf. Model., 2025)

SI Data for "Computation of Protein-Ligand Binding Free Energies with a Quantum Mechanics based Mining Minima Algorithm". - Megan Schlinsog; Tosaporn Sattasathuchana; Peng Xu; Emilie Guidez; Michael K. Gilson; Potter Michael; Mark S. Gordon; Simon Webb (Zenodo, 2025)