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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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