Michael K. Gilson

Publication Activity (10 Years)

Years Active: 1991-2024
Publications (10 Years): 26

Top Topics

Protein Tertiary Structure

Lessons Learned

Grand Challenge

Top Venues

J. Comput. Aided Mol. Des.

J. Chem. Inf. Model.

J. Comput. Chem.

Publications

Peter Eckmann, Jake Anderson, Rose Yu, Michael K. Gilson
Ligand-Based Compound Activity Prediction via Few-Shot Learning. J. Chem. Inf. Model. 64 (14) (2024)
Peter Eckmann, Dongxia Wu, Germano Heinzelmann, Michael K. Gilson, Rose Yu
MFBind: a Multi-Fidelity Approach for Evaluating Drug Compounds in Practical Generative Modeling. CoRR (2024)
Vineet Thumuluri, Peter Eckmann, Michael K. Gilson, Rose Yu
Technical report: Improving the properties of molecules generated by LIMO. CoRR (2024)
Peter Eckmann, Jake Anderson, Michael K. Gilson, Rose Yu
Target-Free Compound Activity Prediction via Few-Shot Learning. CoRR (2023)
Peter Eckmann, Kunyang Sun, Bo Zhao, Mudong Feng, Michael K. Gilson, Rose Yu
LIMO: Latent Inceptionism for Targeted Molecule Generation. CoRR (2022)
Peter Eckmann, Kunyang Sun, Bo Zhao, Mudong Feng, Michael K. Gilson, Rose Yu
LIMO: Latent Inceptionism for Targeted Molecule Generation. ICML (2022)
Sergio A. Pinacho-Castellanos, César R. García-Jacas, Michael K. Gilson, Carlos A. Brizuela
Correction to Alignment-Free Antimicrobial Peptide Predictors: Improving Performance by a Thorough Analysis of the Largest Available Data Set. J. Chem. Inf. Model. 61 (7) (2021)
Teresa Danielle Bergazin, Ido Y. Ben-Shalom, Nathan M. Lim, Sam C. Gill, Michael K. Gilson, David L. Mobley
Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo. J. Comput. Aided Mol. Des. 35 (2) (2021)
K. Kellett, David R. Slochower, Michael Schauperl, B. M. Duggan, Michael K. Gilson
Experimental characterization of the association of β-cyclodextrin and eight novel cyclodextrin derivatives with two guest compounds. J. Comput. Aided Mol. Des. 35 (1) (2021)
Sergio A. Pinacho-Castellanos, César R. García-Jacas, Michael K. Gilson, Carlos A. Brizuela
Alignment-Free Antimicrobial Peptide Predictors: Improving Performance by a Thorough Analysis of the Largest Available Data Set. J. Chem. Inf. Model. 61 (6) (2021)
Joel Ricci-Lopez, Sergio A. Aguila, Michael K. Gilson, Carlos A. Brizuela
Improving Structure-Based Virtual Screening with Ensemble Docking and Machine Learning. J. Chem. Inf. Model. 61 (11) (2021)
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
The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. J. Comput. Aided Mol. Des. 34 (5) (2020)
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
D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. J. Comput. Aided Mol. Des. 34 (2) (2020)
Michael K. Gilson, Rommie E. Amaro
Drug Design Data Resource, Grand Challenge 4, second of two issues. J. Comput. Aided Mol. Des. 34 (2) (2020)
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
D3R Grand Challenge 3: blind prediction of protein-ligand poses and affinity rankings. J. Comput. Aided Mol. Des. 33 (1) (2019)
Michael K. Gilson
This issue: Drug Design Data Resource Grand Challenge 4, first of two issues. J. Comput. Aided Mol. Des. 33 (12) (2019)
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
D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. J. Comput. Aided Mol. Des. 32 (1) (2018)
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
Overview of the SAMPL6 host-guest binding affinity prediction challenge. J. Comput. Aided Mol. Des. 32 (10) (2018)
Michael R. Shirts, Christoph Klein, Jason M. Swails, Jian Yin, Michael K. Gilson, David L. Mobley, David A. Case, Ellen D. Zhong
Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. J. Comput. Aided Mol. Des. 31 (8) (2017)
Jian Yin, Niel M. Henriksen, David R. Slochower, Michael R. Shirts, Michael Chiu, David L. Mobley, Michael K. Gilson
Overview adcm43.bhtof the SAMPL5 host-guest challenge: Are we doing better? J. Comput. Aided Mol. Des. 31 (1) (2017)
Michael R. Shirts, Christoph Klein, Jason M. Swails, Jian Yin, Michael K. Gilson, David L. Mobley, David A. Case, Ellen D. Zhong
Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. J. Comput. Aided Mol. Des. 31 (1) (2017)
Jian Yin, Niel M. Henriksen, David R. Slochower, Michael K. Gilson
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. 31 (1) (2017)
Steven Ramsey, Crystal Nguyen, Romelia Salomón-Ferrer, Ross C. Walker, Michael K. Gilson, Tom Kurtzman
Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST. J. Comput. Chem. 37 (21) (2016)
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
D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions. J. Comput. Aided Mol. Des. 30 (9) (2016)
Caitlin C. Bannan, Kalistyn H. Burley, Michael Chiu, Michael R. Shirts, Michael K. Gilson, David L. Mobley
Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge. J. Comput. Aided Mol. Des. 30 (11) (2016)
Michael K. Gilson, Tiqing Liu, Michael Baitaluk, George Nicola, Linda Hwang, Jenny Chong
BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology. Nucleic Acids Res. 44 (Database-Issue) (2016)
George Nicola, Michael R. Berthold, Michael P. Hedrick, Michael K. Gilson
Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME. Database J. Biol. Databases Curation 2015 (2015)
Hari S. Muddana, Andrew T. Fenley, David L. Mobley, Michael K. Gilson
The SAMPL4 host-guest blind prediction challenge: an overview. J. Comput. Aided Mol. Des. 28 (4) (2014)
Hari S. Muddana, Jian Yin, Neil V. Sapra, Andrew T. Fenley, Michael K. Gilson
Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method. J. Comput. Aided Mol. Des. 28 (4) (2014)
Hari S. Muddana, Neil V. Sapra, Andrew T. Fenley, Michael K. Gilson
The SAMPL4 hydration challenge: evaluation of partial charge sets with explicit-water molecular dynamics simulations. J. Comput. Aided Mol. Des. 28 (3) (2014)
Camilo Velez-Vega, Michael K. Gilson
Overcoming dissipation in the calculation of standard binding free energies by ligand extraction. J. Comput. Chem. 34 (27) (2013)
Nikolai Hecker, Jessica Ahmed, Joachim von Eichborn, Mathias Dunkel, Karel Macha, Andreas Eckert, Michael K. Gilson, Philip E. Bourne, Robert Preissner
SuperTarget goes quantitative: update on drug-target interactions. Nucleic Acids Res. 40 (Database-Issue) (2012)
Hari S. Muddana, Michael K. Gilson
Prediction of SAMPL3 host-guest binding affinities: evaluating the accuracy of generalized force-fields. J. Comput. Aided Mol. Des. 26 (5) (2012)
Hari S. Muddana, C. Daniel Varnado, Christopher W. Bielawski, Adam R. Urbach, Lyle Isaacs, Matthew T. Geballe, Michael K. Gilson
Blind prediction of host-guest binding affinities: a new SAMPL3 challenge. J. Comput. Aided Mol. Des. 26 (5) (2012)
Vladimir Hnizdo, Michael K. Gilson
Thermodynamic and Differential Entropy under a Change of Variables. Entropy 12 (3) (2010)
Vladimir Hnizdo, Jun Tan, Benjamin J. Killian, Michael K. Gilson
Efficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methods. J. Comput. Chem. 29 (10) (2008)
Wei Chen, Michael K. Gilson
, 425-434 (2007)]. J. Chem. Inf. Model. 47 (5) (2007)
Wei Chen, Michael K. Gilson
ConCept: de Novo Design of Synthetic Receptors for Targeted Ligands. J. Chem. Inf. Model. 47 (2) (2007)
Tiqing Liu, Yuhmei Lin, Xin Wen, Robert N. Jorissen, Michael K. Gilson
BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res. 35 (Database-Issue) (2007)
Visvaldas Kairys, Miguel X. Fernandes, Michael K. Gilson
Screening Drug-Like Compounds by Docking to Homology Models: A Systematic Study. J. Chem. Inf. Model. 46 (1) (2006)
Robert N. Jorissen, Michael K. Gilson
Virtual Screening of Molecular Databases Using a Support Vector Machine. J. Chem. Inf. Model. 45 (3) (2005)
Wei Chen, Jing Huang, Michael K. Gilson
Identification of Symmetries in Molecules and Complexes. J. Chem. Inf. Model. 44 (4) (2004)
Miguel X. Fernandes, Visvaldas Kairys, Michael K. Gilson
Comparing Ligand Interactions with Multiple Receptors via Serial Docking. J. Chem. Inf. Model. 44 (6) (2004)
Michael K. Gilson, Hillary S. R. Gilson, Michael J. Potter
Fast Assignment of Accurate Partial Atomic Charges: An Electronegativity Equalization Method that Accounts for Alternate Resonance Forms. J. Chem. Inf. Comput. Sci. 43 (6) (2003)
Chia-En Chang, Michael K. Gilson
Tork: Conformational analysis method for molecules and complexes. J. Comput. Chem. 24 (16) (2003)
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
ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res. 31 (1) (2003)
Ray Luo, Laurent David, Michael K. Gilson
Accelerated Poisson-Boltzmann calculations for static and dynamic systems. J. Comput. Chem. 23 (13) (2002)
Xi Chen, Yuhmei Lin, Ming Liu, Michael K. Gilson
The Binding Database: data management and interface design. Bioinform. 18 (1) (2002)
Visvaldas Kairys, Michael K. Gilson
Enhanced docking with the mining minima optimizer: Acceleration and side-chain flexibility. J. Comput. Chem. 23 (16) (2002)
Laurent David, Ray Luo, Michael K. Gilson
Ligand-receptor docking with the Mining Minima optimizer. J. Comput. Aided Mol. Des. 15 (2) (2001)
Laurent David, Ray Luo, Michael K. Gilson
Comparison of generalized born and poisson models: Energetics and dynamics of HIV protease. J. Comput. Chem. 21 (4) (2000)
Jan Antosiewicz, James M. Briggs, Adrian H. Elcock, Michael K. Gilson, James Andrew McCammon
Computing ionization states of proteins with a detailed charge model. J. Comput. Chem. 17 (14) (1996)
Michael K. Gilson, Barry Honig
The inclusion of electrostatic hydration energies in molecular mechanics calculations. J. Comput. Aided Mol. Des. 5 (1) (1991)