Michael K. Gilson

57 papers A* 2Journal 55

Year	Rank	Type	Title / Venue / Authors
2025	A*	`conf`	MF-LAL: Drug Compound Generation Using Multi-Fidelity Latent Space Active Learning. ICML Peter Eckmann, Dongxia Wu, Germano Heinzelmann, Michael K. Gilson, Rose Yu
2025	J	`jnl`	Relative BAT: An Automated Tool for Relative Binding Free Energy Calculations by the Separated Topologies Approach. J. Chem. Inf. Model. Germano Heinzelmann, David J. Huggins, Michael K. Gilson
2025	J	`jnl`	The Need for Continuing Blinded Pose- and Activity Prediction Benchmarks. J. Chem. Inf. Model. 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
2024	J	`jnl`	Ligand-Based Compound Activity Prediction via Few-Shot Learning. J. Chem. Inf. Model. Peter Eckmann, Jake Anderson, Rose Yu, Michael K. Gilson
2024	J	`jnl`	MF-LAL: Drug Compound Generation Using Multi-Fidelity Latent Space Active Learning. CoRR Peter Eckmann, Dongxia Wu, Germano Heinzelmann, Michael K. Gilson, Rose Yu
2024	J	`jnl`	MFBind: a Multi-Fidelity Approach for Evaluating Drug Compounds in Practical Generative Modeling. CoRR Peter Eckmann, Dongxia Wu, Germano Heinzelmann, Michael K. Gilson, Rose Yu
2024	J	`jnl`	Technical report: Improving the properties of molecules generated by LIMO. CoRR Vineet Thumuluri, Peter Eckmann, Michael K. Gilson, Rose Yu
2023	J	`jnl`	Target-Free Compound Activity Prediction via Few-Shot Learning. CoRR Peter Eckmann, Jake Anderson, Michael K. Gilson, Rose Yu
2022	A*	`conf`	LIMO: Latent Inceptionism for Targeted Molecule Generation. ICML Peter Eckmann, Kunyang Sun, Bo Zhao, Mudong Feng, Michael K. Gilson, Rose Yu
2022	J	`jnl`	LIMO: Latent Inceptionism for Targeted Molecule Generation. CoRR Peter Eckmann, Kunyang Sun, Bo Zhao, Mudong Feng, Michael K. Gilson, Rose Yu
2021	J	`jnl`	Alignment-Free Antimicrobial Peptide Predictors: Improving Performance by a Thorough Analysis of the Largest Available Data Set. J. Chem. Inf. Model. Sergio Alejandro Pinacho-Castellanos, César R. García-Jacas, Michael K. Gilson, Carlos A. Brizuela
2021	J	`jnl`	Correction to Alignment-Free Antimicrobial Peptide Predictors: Improving Performance by a Thorough Analysis of the Largest Available Data Set. J. Chem. Inf. Model. Sergio Alejandro Pinacho-Castellanos, César R. García-Jacas, Michael K. Gilson, Carlos A. Brizuela
2021	J	`jnl`	Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo. J. Comput. Aided Mol. Des. Teresa Danielle Bergazin, Ido Y. Ben-Shalom, Nathan M. Lim, Sam C. Gill, Michael K. Gilson, David L. Mobley
2021	J	`jnl`	Experimental characterization of the association of β-cyclodextrin and eight novel cyclodextrin derivatives with two guest compounds. J. Comput. Aided Mol. Des. K. Kellett, David R. Slochower, Michael Schauperl, B. M. Duggan, Michael K. Gilson
2021	J	`jnl`	Improving Structure-Based Virtual Screening with Ensemble Docking and Machine Learning. J. Chem. Inf. Model. Joel Ricci-Lopez, Sergio A. Aguila, Michael K. Gilson, Carlos A. Brizuela
2020	J	`jnl`	D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. J. Comput. Aided Mol. Des. 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, Stephen K. Burley, Rommie E. Amaro, Michael K. Gilson
2020	J	`jnl`	Drug Design Data Resource, Grand Challenge 4, second of two issues. J. Comput. Aided Mol. Des. Michael K. Gilson, Rommie E. Amaro
2020	J	`jnl`	The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. J. Comput. Aided Mol. Des. 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, Julien Michel, Michael K. Gilson, Michael R. Shirts, David L. Mobley, John D. Chodera
2019	J	`jnl`	D3R Grand Challenge 3: blind prediction of protein-ligand poses and affinity rankings. J. Comput. Aided Mol. Des. 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, Rommie E. Amaro, Michael K. Gilson
2019	J	`jnl`	This issue: Drug Design Data Resource Grand Challenge 4, first of two issues. J. Comput. Aided Mol. Des. Michael K. Gilson
2018	J	`jnl`	D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. J. Comput. Aided Mol. Des. 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, Rommie E. Amaro
2018	J	`jnl`	Overview of the SAMPL6 host-guest binding affinity prediction challenge. J. Comput. Aided Mol. Des. Andrea Rizzi, Steven Murkli, John N. McNeill, Wei Yao, Matthew R. Sullivan, Michael K. Gilson, Michael Chiu, Lyle Isaacs, Bruce C. Gibb, David L. Mobley, John D. Chodera
2017	J	`jnl`	Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. J. Comput. Aided Mol. Des. Michael R. Shirts, Christoph Klein, Jason M. Swails, Jian Yin, Michael K. Gilson, David L. Mobley, David A. Case, Ellen D. Zhong
2017	J	`jnl`	Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. J. Comput. Aided Mol. Des. Michael R. Shirts, Christoph Klein, Jason M. Swails, Jian Yin, Michael K. Gilson, David L. Mobley, David A. Case, Ellen D. Zhong
2017	J	`jnl`	Overview adcm43.bhtof the SAMPL5 host-guest challenge: Are we doing better? J. Comput. Aided Mol. Des. Jian Yin, Niel M. Henriksen, David R. Slochower, Michael R. Shirts, Michael Chiu, David L. Mobley, Michael K. Gilson
2017	J	`jnl`	The SAMPL5 host-guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method. J. Comput. Aided Mol. Des. Jian Yin, Niel M. Henriksen, David R. Slochower, Michael K. Gilson
2016	J	`jnl`	BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology. Nucleic Acids Res. Michael K. Gilson, Tiqing Liu, Michael Baitaluk, George Nicola, Linda Hwang, Jenny Chong
2016	J	`jnl`	Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge. J. Comput. Aided Mol. Des. Caitlin C. Bannan, Kalistyn H. Burley, Michael Chiu, Michael R. Shirts, Michael K. Gilson, David L. Mobley
2016	J	`jnl`	D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions. J. Comput. Aided Mol. Des. 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, Rommie E. Amaro, Victoria A. Feher, Michael K. Gilson
2016	J	`jnl`	Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST. J. Comput. Chem. Steven Ramsey, Crystal Nguyen, Romelia Salomón-Ferrer, Ross C. Walker, Michael K. Gilson, Tom Kurtzman
2015	J	`jnl`	Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME. Database J. Biol. Databases Curation George Nicola, Michael R. Berthold, Michael P. Hedrick, Michael K. Gilson
2014	J	`jnl`	Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method. J. Comput. Aided Mol. Des. Hari S. Muddana, Jian Yin, Neil V. Sapra, Andrew T. Fenley, Michael K. Gilson
2014	J	`jnl`	The SAMPL4 host-guest blind prediction challenge: an overview. J. Comput. Aided Mol. Des. Hari S. Muddana, Andrew T. Fenley, David L. Mobley, Michael K. Gilson
2014	J	`jnl`	The SAMPL4 hydration challenge: evaluation of partial charge sets with explicit-water molecular dynamics simulations. J. Comput. Aided Mol. Des. Hari S. Muddana, Neil V. Sapra, Andrew T. Fenley, Michael K. Gilson
2013	J	`jnl`	Overcoming dissipation in the calculation of standard binding free energies by ligand extraction. J. Comput. Chem. Camilo Velez-Vega, Michael K. Gilson
2012	J	`jnl`	Blind prediction of host-guest binding affinities: a new SAMPL3 challenge. J. Comput. Aided Mol. Des. Hari S. Muddana, C. Daniel Varnado, Christopher W. Bielawski, Adam R. Urbach, Lyle Isaacs, Matthew T. Geballe, Michael K. Gilson
2012	J	`jnl`	Prediction of SAMPL3 host-guest binding affinities: evaluating the accuracy of generalized force-fields. J. Comput. Aided Mol. Des. Hari S. Muddana, Michael K. Gilson
2012	J	`jnl`	SuperTarget goes quantitative: update on drug-target interactions. Nucleic Acids Res. Nikolai Hecker, Jessica Ahmed, Joachim von Eichborn, Mathias Dunkel, Karel Macha, Andreas Eckert, Michael K. Gilson, Philip E. Bourne, Robert Preissner
2010	J	`jnl`	Thermodynamic and Differential Entropy under a Change of Variables. Entropy Vladimir Hnizdo, Michael K. Gilson
2008	J	`jnl`	Efficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methods. J. Comput. Chem. Vladimir Hnizdo, Jun Tan, Benjamin J. Killian, Michael K. Gilson
2007	J	`jnl`	BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res. Tiqing Liu, Yuhmei Lin, Xin Wen, Robert N. Jorissen, Michael K. Gilson
2007	J	`jnl`	ConCept: de Novo Design of Synthetic Receptors for Targeted Ligands [ J. Chem. Inf. Model. Wei Chen, Michael K. Gilson
2007	J	`jnl`	ConCept: de Novo Design of Synthetic Receptors for Targeted Ligands. J. Chem. Inf. Model. Wei Chen, Michael K. Gilson
2006	J	`jnl`	Screening Drug-Like Compounds by Docking to Homology Models: A Systematic Study. J. Chem. Inf. Model. Visvaldas Kairys, Miguel X. Fernandes, Michael K. Gilson
2005	J	`jnl`	Virtual Screening of Molecular Databases Using a Support Vector Machine. J. Chem. Inf. Model. Robert N. Jorissen, Michael K. Gilson
2004	J	`jnl`	Comparing Ligand Interactions with Multiple Receptors via Serial Docking. J. Chem. Inf. Model. Miguel X. Fernandes, Visvaldas Kairys, Michael K. Gilson
2004	J	`jnl`	Identification of Symmetries in Molecules and Complexes. J. Chem. Inf. Model. Wei Chen, Jing Huang, Michael K. Gilson
2003	J	`jnl`	ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res. 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
2003	J	`jnl`	Fast Assignment of Accurate Partial Atomic Charges: An Electronegativity Equalization Method that Accounts for Alternate Resonance Forms. J. Chem. Inf. Comput. Sci. Michael K. Gilson, Hillary S. R. Gilson, Michael J. Potter
2003	J	`jnl`	Tork: Conformational analysis method for molecules and complexes. J. Comput. Chem. Chia-En Chang, Michael K. Gilson
2002	J	`jnl`	Accelerated Poisson-Boltzmann calculations for static and dynamic systems. J. Comput. Chem. Ray Luo, Laurent David, Michael K. Gilson
2002	J	`jnl`	Enhanced docking with the mining minima optimizer: Acceleration and side-chain flexibility. J. Comput. Chem. Visvaldas Kairys, Michael K. Gilson
2002	J	`jnl`	The Binding Database: data management and interface design. Bioinform. Xi Chen, Yuhmei Lin, Ming Liu, Michael K. Gilson
2001	J	`jnl`	Ligand-receptor docking with the Mining Minima optimizer. J. Comput. Aided Mol. Des. Laurent David, Ray Luo, Michael K. Gilson
2000	J	`jnl`	Comparison of generalized born and poisson models: Energetics and dynamics of HIV protease. J. Comput. Chem. Laurent David, Ray Luo, Michael K. Gilson
1996	J	`jnl`	Computing ionization states of proteins with a detailed charge model. J. Comput. Chem. Jan Antosiewicz, James M. Briggs, Adrian H. Elcock, Michael K. Gilson, James Andrew McCammon
1991	J	`jnl`	The inclusion of electrostatic hydration energies in molecular mechanics calculations. J. Comput. Aided Mol. Des. Michael K. Gilson, Barry Honig