Michael K Gilson (M K Gilson)

Publication Activity (10 Years)

Years Active: 2015-2024
Publications (10 Years): 65

Top Topics

Human Serum Albumin

Machine Learning

Molecular Dynamics

Top Venues

Journal of chemical theory and computation

Journal of chemical information and modeling

Physical chemistry chemical physics : PCCP

The journal of physical chemistry. B

This page only lists publications with an associated author ORCID identifier.

Publications

Peter Eckmann, Jake Anderson, Rose Yu, Michael K Gilson
Ligand-Based Compound Activity Prediction via Few-Shot Learning. Journal of chemical information and modeling 64 (14) (2024)
Brenda Andrade, Ashley Chen, Michael K Gilson
Host-guest systems for the SAMPL9 blinded prediction challenge: phenothiazine as a privileged scaffold for binding to cyclodextrins. Physical chemistry chemical physics : PCCP 26 (3) (2024)
Michael K Gilson, Lawrence E Stewart, Michael J Potter, Simon P Webb
Rapid, Accurate, Ranking of Protein-Ligand Binding Affinities with VM2, the Second-Generation Mining Minima Method. Journal of chemical theory and computation 20 (14) (2024)
Lily Wang, Pavan Kumar Behara, Matthew W Thompson, Trevor Gokey, Yuanqing Wang, Jeffrey R Wagner, Daniel J Cole, Michael K Gilson, Michael R Shirts, David L Mobley
The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling. The journal of physical chemistry. B 128 (29) (2024)
Liangyue Wang, Michael Schauperl, David L Mobley, Christopher Bayly, Michael K Gilson
A Fast, Convenient, Polarizable Electrostatic Model for Molecular Dynamics. Journal of chemical theory and computation 20 (3) (2024)
Liangyue Wang, Michael Schauperl, David L Mobley, Christopher Bayly, Michael K Gilson
A Fast, Convenient, Polarizable Electrostatic Model for Molecular Dynamics. Journal of chemical theory and computation 20 (3) (2024)
Germano Heinzelmann, David J Huggins, Michael K Gilson
BAT2: an Open-Source Tool for Flexible, Automated, and Low Cost Absolute Binding Free Energy Calculations. Journal of chemical theory and computation (2024)
Michael K Gilson, Tom Kurtzman
Free Energy Density of a Fluid and Its Role in Solvation and Binding. Journal of chemical theory and computation 20 (7) (2024)
Brenda Andrade, Ashley Chen, Michael K Gilson
Host-guest systems for the SAMPL9 blinded prediction challenge: phenothiazine as a privileged scaffold for binding to cyclodextrins. Physical chemistry chemical physics : PCCP 26 (3) (2024)
Peter Eckmann, Jake Anderson, Rose Yu, Michael K Gilson
Ligand-Based Compound Activity Prediction via Few-Shot Learning. Journal of chemical information and modeling 64 (14) (2024)
Michael K Gilson, Tom Kurtzman
Free Energy Density of a Fluid and Its Role in Solvation and Binding. Journal of chemical theory and computation 20 (7) (2024)
Lily Wang, Pavan Kumar Behara, Matthew W Thompson, Trevor Gokey, Yuanqing Wang, Jeffrey R Wagner, Daniel J Cole, Michael K Gilson, Michael R Shirts, David L Mobley
The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling. The journal of physical chemistry. B (2024)
Brenda Andrade, Ashley Chen, Michael K Gilson
Host-guest systems for the SAMPL9 blinded prediction challenge: phenothiazine as a privileged scaffold for binding to cyclodextrins. Physical chemistry chemical physics : PCCP 26 (3) (2024)
Michael K Gilson, Lawrence E Stewart, Michael J Potter, Simon P Webb
Rapid, Accurate, Ranking of Protein-Ligand Binding Affinities with VM2, the Second-Generation Mining Minima Method. Journal of chemical theory and computation (2024)
Brenda Andrade, Ashley Chen, Michael K Gilson
Host-guest systems for the SAMPL9 blinded prediction challenge: phenothiazine as a privileged scaffold for binding to cyclodextrins. Physical chemistry chemical physics : PCCP 26 (3) (2024)
Brenda Andrade, Ashley Chen, Michael K Gilson
Host-guest systems for the SAMPL9 blinded prediction challenge: phenothiazine as a privileged scaffold for binding to cyclodextrins. Physical chemistry chemical physics : PCCP 26 (3) (2024)
Lily Wang, Pavan Kumar Behara, Matthew W Thompson, Trevor Gokey, Yuanqing Wang, Jeffrey R Wagner, Daniel J Cole, Michael K Gilson, Michael R Shirts, David L Mobley
The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling. The journal of physical chemistry. B 128 (29) (2024)
Michael K Gilson, Lawrence E Stewart, Michael J Potter, Simon P Webb
Rapid, Accurate, Ranking of Protein-Ligand Binding Affinities with VM2, the Second-Generation Mining Minima Method. Journal of chemical theory and computation (2024)
Germano Heinzelmann, David J Huggins, Michael K Gilson
BAT2: an Open-Source Tool for Flexible, Automated, and Low Cost Absolute Binding Free Energy Calculations. Journal of chemical theory and computation 20 (15) (2024)
Liangyue Wang, Michael Schauperl, David L Mobley, Christopher Bayly, Michael K Gilson
A Fast, Convenient, Polarizable Electrostatic Model for Molecular Dynamics. Journal of chemical theory and computation 20 (3) (2024)
Peter Eckmann, Jake Anderson, Rose Yu, Michael K Gilson
Ligand-Based Compound Activity Prediction via Few-Shot Learning. Journal of chemical information and modeling (2024)
Germano Heinzelmann, David J Huggins, Michael K Gilson
BAT2: an Open-Source Tool for Flexible, Automated, and Low Cost Absolute Binding Free Energy Calculations. Journal of chemical theory and computation 20 (15) (2024)
Lily Wang, Pavan Kumar Behara, Matthew W Thompson, Trevor Gokey, Yuanqing Wang, Jeffrey R Wagner, Daniel J Cole, Michael K Gilson, Michael R Shirts, David L Mobley
The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling. The journal of physical chemistry. B 128 (29) (2024)
Liangyue Wang, Michael Schauperl, David L Mobley, Christopher Bayly, Michael K Gilson
A Fast, Convenient, Polarizable Electrostatic Model for Molecular Dynamics. Journal of chemical theory and computation (2024)
Peter Eckmann, Jake Anderson, Rose Yu, Michael K Gilson
Ligand-Based Compound Activity Prediction via Few-Shot Learning. Journal of chemical information and modeling 64 (14) (2024)
Germano Heinzelmann, David J Huggins, Michael K Gilson
Correction to "BAT2: an Open-Source Tool for Flexible, Automated, and Low Cost Absolute Binding Free Energy Calculations". Journal of chemical theory and computation (2024)
Lily Wang, Pavan Kumar Behara, Matthew W Thompson, Trevor Gokey, Yuanqing Wang, Jeffrey R Wagner, Daniel J Cole, Michael K Gilson, Michael R Shirts, David L Mobley
The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling. The journal of physical chemistry. B 128 (29) (2024)
Michael K Gilson, Tom Kurtzman
Free Energy Density of a Fluid and Its Role in Solvation and Binding. Journal of chemical theory and computation (2024)
Liangyue Wang, Michael Schauperl, David L Mobley, Christopher Bayly, Michael K Gilson
A Fast, Convenient, Polarizable Electrostatic Model for Molecular Dynamics. Journal of chemical theory and computation 20 (3) (2024)
Germano Heinzelmann, David J Huggins, Michael K Gilson
BAT2: an Open-Source Tool for Flexible, Automated, and Low Cost Absolute Binding Free Energy Calculations. Journal of chemical theory and computation 20 (15) (2024)
Peter Eckmann, Jake Anderson, Rose Yu, Michael K Gilson
Ligand-Based Compound Activity Prediction via Few-Shot Learning. Journal of chemical information and modeling (2024)
Jehad Almaliti, Pavla Fajtova, Jaeson Santos Calla-Choque, Gregory M LaMonte, Mudong Feng, Frances Rocamora, Sabine Ottilie, Evgenia Glukhov, Evzen Boura, Raymond T Suhandynata, Jeremiah D Momper, Michael K Gilson, Elizabeth A Winzeler, William H Gerwick, Anthony J O'Donoghue
Development of Potent and Highly Selective Epoxyketone-Based Plasmodium Proteasome Inhibitors. Chemistry (Weinheim an der Bergstrasse, Germany) (2023)
Jeffry Setiadi, Simon Boothroyd, David R Slochower, David L Dotson, Matthew W Thompson, Jeffrey R Wagner, Lee-Ping Wang, Michael K Gilson
Tuning Potential Functions to Host-Guest Binding Data. Journal of chemical theory and computation (2023)
Jeffry Setiadi, Simon Boothroyd, David R Slochower, David L Dotson, Matthew W Thompson, Jeffrey R Wagner, Lee-Ping Wang, Michael K Gilson
Tuning Potential Functions to Host-Guest Binding Data. Journal of chemical theory and computation 20 (1) (2023)
Simon Boothroyd, Pavan Kumar Behara, Owen C Madin, David F Hahn, Hyesu Jang, Vytautas Gapsys, Jeffrey R Wagner, Joshua T Horton, David L Dotson, Matthew W Thompson, Jessica Maat, Trevor Gokey, Lee-Ping Wang, Daniel J Cole, Michael K Gilson, John D Chodera, Christopher I Bayly, Michael R Shirts, David L Mobley
Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field. Journal of chemical theory and computation (2023)
Jeffry Setiadi, Simon Boothroyd, David R Slochower, David L Dotson, Matthew W Thompson, Jeffrey R Wagner, Lee-Ping Wang, Michael K Gilson
Tuning Potential Functions to Host-Guest Binding Data. Journal of chemical theory and computation 20 (1) (2023)
Laura M Grimm, Jeffry Setiadi, Boryslav Tkachenko, Peter Richard Schreiner, Michael K Gilson, Frank Biedermann
The temperature-dependence of host-guest binding thermodynamics: experimental and simulation studies. Chemical science 14 (42) (2023)
Brenda Andrade, Ashley Chen, Michael K Gilson
Host-guest systems for the SAMPL9 blinded prediction challenge: phenothiazine as a privileged scaffold for binding to cyclodextrins. Physical chemistry chemical physics : PCCP (2023)
Jeffry Setiadi, Simon Boothroyd, David R Slochower, David L Dotson, Matthew W Thompson, Jeffrey R Wagner, Lee-Ping Wang, Michael K Gilson
Tuning Potential Functions to Host-Guest Binding Data. Journal of chemical theory and computation 20 (1) (2023)
Joel Ricci-Lopez, Sergio A Aguila, Michael K Gilson, Carlos A Brizuela
Improving Structure-Based Virtual Screening with Ensemble Docking and Machine Learning. Journal of chemical information and modeling 61 (11) (2021)
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. Journal of chemical information and modeling 61 (7) (2021)
Ido Y Ben Shalom, Charles Lin, Brian K Radak, Woody Sherman, Michael K Gilson
Fast Equilibration of Water between Buried Sites and the Bulk by Molecular Dynamics with Parallel Monte Carlo Water Moves on Graphical Processing Units. Journal of chemical theory and computation (2021)
Yudong Qiu, Daniel G A Smith, Simon Boothroyd, Hyesu Jang, David F Hahn, Jeffrey Wagner, Caitlin C Bannan, Trevor Gokey, Victoria T Lim, Chaya D Stern, Andrea Rizzi, Bryon Tjanaka, Gary John Tresadern, Xavier Lucas, Michael R Shirts, Michael K Gilson, John D Chodera, Christopher I Bayly, David L Mobley, Lee-Ping Wang
Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field. Journal of chemical theory and computation 17 (10) (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. Journal of computer-aided molecular design 34 (5) (2020)
Ido Y Ben Shalom, Zhixiong Lin, Brian K Radak, Charles Lin, Woody Sherman, Michael K Gilson
Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations. Journal of chemical theory and computation 16 (12) (2020)
Sophie M Kantonen, Hari S Muddana, Michael Schauperl, Niel M Henriksen, Lee-Ping Wang, Michael K Gilson
Data-Driven Mapping of Gas-Phase Quantum Calculations to General Force Field Lennard-Jones Parameters. Journal of chemical theory and computation 16 (2) (2020)
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. Journal of computer-aided molecular design 35 (2) (2020)
K Kellett, D R Slochower, M Schauperl, B M Duggan, Michael K Gilson
Experimental characterization of the association of β-cyclodextrin and eight novel cyclodextrin derivatives with two guest compounds. Journal of computer-aided molecular design 35 (1) (2020)
Conor D Parks, Zied Gaieb, Michael Chiu, Huanwang Yang, Chenghua Shao, W Patrick Walters, Johanna M Jansen, Georgia McGaughey, Richard A Lewis, Scott D Bembenek, Michael K Ameriks, Tara Mirzadegan, Stephen K Burley, Rommie Elizabeth Amaro, Michael K Gilson
D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. Journal of computer-aided molecular design 34 (2) (2020)
Cassandra E Callmann, Clare L M LeGuyader, Spencer T Burton, Matthew P Thompson, Robert Hennis, Christopher Barback, Niel M Henriksen, Warren C Chan, Matt J Jaremko, Jin Yang, Arnold Garcia, Michael D Burkart, Michael K Gilson, Jeremiah D Momper, Paul A Bertin, Nathan C Gianneschi
Antitumor Activity of 1,18-Octadecanedioic Acid-Paclitaxel Complexed with Human Serum Albumin. Journal of the American Chemical Society 141 (30) (2019)
David R Slochower, Niel M Henriksen, Lee-Ping Wang, John D Chodera, David L Mobley, Michael K Gilson
Binding Thermodynamics of Host-Guest Systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative. Journal of chemical theory and computation 15 (11) (2019)
Young Hun Kim, Geoffray Leriche, Karthik Diraviyam, Takaoki Koyanagi, Kai-Fu Gao, David Onofrei, Joseph Patterson, Anirvan Guha, Nathan C Gianneschi, Gregory P Holland, Michael K Gilson, Michael Mayer, David Sept, Jerry Yang
Entropic effects enable life at extreme temperatures. Science advances 5 (5) (2019)
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 Elizabeth Amaro, Michael K Gilson
D3R Grand Challenge 3: blind prediction of protein-ligand poses and affinity rankings. Journal of computer-aided molecular design 33 (1) (2019)
Ido Y Ben Shalom, Charles Lin, Tom Kurtzman, Ross C Walker, Michael K Gilson
Simulating Water Exchange to Buried Binding Sites. Journal of chemical theory and computation 15 (4) (2019)
Camila Zanette, Caitlin C Bannan, Christopher I Bayly, Josh Fass, Michael K Gilson, Michael R Shirts, John D Chodera, David L Mobley
Toward Learned Chemical Perception of Force Field Typing Rules. Journal of chemical theory and computation 15 (1) (2018)
Lorillee Tallorin, JiaLei Wang, Woojoo E Kim, Swagat Sahu, Nicolas M Kosa, Pu Yang, Matthew Thompson, Michael K Gilson, Peter I Frazier, Michael D Burkart, Nathan C Gianneschi
Discovering de novo peptide substrates for enzymes using machine learning. Nature communications 9 (1) (2018)
Amanda Li, Michael K Gilson
Protein-ligand binding enthalpies from near-millisecond simulations: Analysis of a preorganization paradox. The Journal of chemical physics 149 (7) (2018)
Jian Yin, Niel M Henriksen, Hari S Muddana, Michael K Gilson
Bind3P: Optimization of a Water Model Based on Host-Guest Binding Data. Journal of chemical theory and computation 14 (7) (2018)
Andrea Rizzi, Steven Murkli, J Nolan McNeill, Wei Yao, Matthew Sullivan, Michael K Gilson, Michael W Chiu, Lyle D Isaacs, Anthony Wishard, David L Mobley, John D Chodera
Overview of the SAMPL6 host-guest binding affinity prediction challenge. Journal of computer-aided molecular design 32 (10) (2018)
Shin-Fu Chen, Nan-Lan Huang, Jung-Hsin Lin, Chyuan-Chuan Wu, Ying-Ren Wang, Yu-Jen Yu, Michael K Gilson, Nei-Li Chan
Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate. Nature communications 9 (1) (2018)
Kamran Haider, Anthony Cruz, Steven Ramsey, Michael K Gilson, Tom Kurtzman
Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories. Journal of chemical theory and computation 14 (1) (2017)
Ofer Reany, Amanda Li, Maayan Yefet, Michael K Gilson, Ehud Keinan
Attractive Interactions between Heteroallenes and the Cucurbituril Portal. Journal of the American Chemical Society 139 (24) (2017)
Niel M Henriksen, Michael K Gilson
Evaluating Force Field Performance in Thermodynamic Calculations of Cyclodextrin Host-Guest Binding: Water Models, Partial Charges, and Host Force Field Parameters. Journal of chemical theory and computation 13 (9) (2017)
Germano Heinzelmann, Niel M Henriksen, Michael K Gilson
Attach-Pull-Release Calculations of Ligand Binding and Conformational Changes on the First BRD4 Bromodomain. Journal of chemical theory and computation 13 (7) (2017)
Khaleel I Assaf, Mara Florea, Jens Antony, Niel M Henriksen, Jian Yin, Andreas Hansen, Zheng-Wang Qu, Rebecca Sure, Dieter Klapstein, Michael K Gilson, Stefan Grimme, Werner M Nau
HYDROPHOBE Challenge: A Joint Experimental and Computational Study on the Host-Guest Binding of Hydrocarbons to Cucurbiturils, Allowing Explicit Evaluation of Guest Hydration Free-Energy Contributions. The journal of physical chemistry. B 121 (49) (2017)
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 research 44 (D1) (2015)