Works by Gilson, Michael K.

Results: 50

Parameterization of an effective potential for protein-ligand binding from host-guest affinity data.

Published in:

Journal of Molecular Recognition, 2016, v. 29, n. 1, p. 10, doi. 10.1002/jmr.2489

By:

Wickstrom, Lauren;
Deng, Nanjie;
He, Peng;
Mentes, Ahmet;
Nguyen, Crystal;
Gilson, Michael K.;
Kurtzman, Tom;
Gallicchio, Emilio;
Levy, Ronald M.

Publication type:

Article

The bioinformatics of molecular recognition.

Published in:

Journal of Molecular Recognition, 2002, v. 15, n. 1, p. 1, doi. 10.1002/jmr.560

By:

Gilson, Michael K.

Publication type:

Article

Development of Potent and Highly Selective Epoxyketone‐Based Plasmodium Proteasome Inhibitors.

Published in:

Chemistry - A European Journal, 2023, v. 29, n. 20, p. 1, doi. 10.1002/chem.202203958

By:

Almaliti, Jehad;
Fajtová, Pavla;
Calla, Jaeson;
LaMonte, Gregory M.;
Feng, Mudong;
Rocamora, Frances;
Ottilie, Sabine;
Glukhov, Evgenia;
Boura, Evzen;
Suhandynata, Raymond T.;
Momper, Jeremiah D.;
Gilson, Michael K.;
Winzeler, Elizabeth A.;
Gerwick, William H.;
O'Donoghue, Anthony J.

Publication type:

Article

Stimuli Induced Uptake of Protein‐Like Peptide Brush Polymers.

Published in:

Chemistry - A European Journal, 2022, v. 28, n. 5, p. 1, doi. 10.1002/chem.202103438

By:

Blum, Angela P.;
Yin, Jian;
Lin, Helen H.;
Oliver, Blayne A.;
Kammeyer, Jacquelin K.;
Thompson, Matthew P.;
Gilson, Michael K.;
Gianneschi, Nathan C.

Publication type:

Article

SuperTarget goes quantitative: update on drug–target interactions.

Published in:

Nucleic Acids Research, 2012, p. D1113, doi. 10.1093/nar/gkr912

By:

Hecker, Nikolai;
Ahmed, Jessica;
von Eichborn, Joachim;
Dunkel, Mathias;
Macha, Karel;
Eckert, Andreas;
Gilson, Michael K.;
Bourne, Philip E.;
Preissner, Robert

Publication type:

Article

BindingDB: a web-accessible database of experimentally determined protein–ligand binding affinities.

Published in:

Nucleic Acids Research, 2007, v. 35, p. d198, doi. 10.1093/nar/gkl999

By:

Liu, Tiqing;
Lin, Yuhmei;
Wen, Xin;
Jorissen, Robert N.;
Gilson, Michael K.

Publication type:

Article

A hierarchical method for generating low-energy conformers of a protein-ligand complex.

Published in:

Proteins, 1998, v. 33, n. 4, p. 475, doi. 10.1002/(SICI)1097-0134(19981201)33:4<475::AID-PROT3>3.0.CO;2-B

By:

Given, James A.;
Gilson, Michael K.

Publication type:

Article

Multiple-site titration and molecular modeling: Two rapid methods for computing energies and forces for ionizable groups in proteins.

Published in:

Proteins, 1993, v. 15, n. 3, p. 266, doi. 10.1002/prot.340150305

By:

Gilson, Michael K.

Publication type:

Article

Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis.

Published in:

Proteins, 1988, v. 4, n. 1, p. 7, doi. 10.1002/prot.340040104

By:

Gilson, Michael K.;
Honig, Barry

Publication type:

Article

Energetics of charge-charge interactions in proteins.

Published in:

Proteins, 1988, v. 3, n. 1, p. 32, doi. 10.1002/prot.340030104

By:

Gilson, Michael K.;
Honig, Barry H.

Publication type:

Article

The Binding Database: data management and interface design.

Published in:

Bioinformatics, 2002, v. 18, n. 1, p. 130, doi. 10.1093/bioinformatics/18.1.130

By:

Chen, Xi;
Lin, Yuhmei;
Liu, Ming;
Gilson, Michael K.

Publication type:

Article

Absolute binding free energy calculations improve enrichment of actives in virtual compound screening.

Published in:

Scientific Reports, 2022, v. 12, n. 1, p. 1, doi. 10.1038/s41598-022-17480-w

By:

Feng, Mudong;
Heinzelmann, Germano;
Gilson, Michael K.

Publication type:

Article

Computing ionization states of proteins with a detailed charge model.

Published in:

Journal of Computational Chemistry, 1996, v. 17, n. 14, p. 1633, doi. 10.1002/(SICI)1096-987X(19961115)17:14<1633::AID-JCC5>3.0.CO;2-M

By:

Antosiewicz, Jan;
Briggs, James M.;
Elcock, Adrian H.;
Gilson, Michael K.;
McCammon, J. Andrew

Publication type:

Article

Molecular dynamics simulation with a continuum electrostatic model of the solvent.

Published in:

Journal of Computational Chemistry, 1995, v. 16, n. 9, p. 1081, doi. 10.1002/jcc.540160904

By:

Gilson, Michael K.;
McCammon, J. Andrew;
Madura, Jeffry D.

Publication type:

Article

Calculating the electrostatic potential of molecules in solution: Method and error assessment.

Published in:

Journal of Computational Chemistry, 1988, v. 9, n. 4, p. 327, doi. 10.1002/jcc.540090407

By:

Gilson, Michael K.;
Sharp, Kim A.;
Honig, Barry H.

Publication type:

Article

Ten Years of Standardizing Proteomic Data: A Report on the HUPO-PSI Spring Workshop.

Published in:

Proteomics, 2012, v. 12, n. 18, p. 2767, doi. 10.1002/pmic.201270126

By:

Orchard, Sandra;
Binz, Pierre-Alain;
Borchers, Christoph;
Gilson, Michael K.;
Jones, Andrew R.;
Nicola, George;
Vizcaino, Juan Antonio;
Deutsch, Eric W.;
Hermjakob, Henning

Publication type:

Article

D3R Grand Challenge 3: blind prediction of protein-ligand poses and affinity rankings.

Published in:

Journal of Computer-Aided Molecular Design, 2019, v. 33, n. 1, p. 1, doi. 10.1007/s10822-018-0180-4

By:

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.;
Amaro, Rommie E.;
Gilson, Michael K.

Publication type:

Article

Overview of the SAMPL6 host-guest binding affinity prediction challenge.

Published in:

Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 10, p. 937, doi. 10.1007/s10822-018-0170-6

By:

Rizzi, Andrea;
Murkli, Steven;
McNeill, John N.;
Yao, Wei;
Sullivan, Matthew;
Gilson, Michael K.;
Chiu, Michael W.;
Isaacs, Lyle;
Gibb, Bruce C.;
Mobley, David L.;
Chodera, John D.

Publication type:

Article

D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.

Published in:

Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 1, doi. 10.1007/s10822-017-0088-4

By:

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.;
Amaro, Rommie E.

Publication type:

Article

Editorial: Molecular recognition databases.

Published in:

Biopolymers, 2001, v. 61, n. 2, p. 97, doi. 10.1002/1097-0282(2001/2002)61:2<97::AID-BIP10074>3.0.CO;2-H

By:

Gilson, Michael K.

Publication type:

Article

The binding database: Overview and user's guide.

Published in:

Biopolymers, 2001, v. 61, n. 2, p. 127, doi. 10.1002/1097-0282(2002)61:2<127::AID-BIP10076>3.0.CO;2-N

By:

Chen, Xi;
Lin, Yuhmei;
Gilson, Michael K.

Publication type:

Article

Calculation of electrostatic potentials in an enzyme active site.

Published in:

Nature, 1987, v. 330, n. 6143, p. 84, doi. 10.1038/330084a0

By:

Gilson, Michael K.;
Honig, Barry H.

Publication type:

Article

Overcoming Dissipation in the Calculation of Standard Binding Free Energies by Ligand Extraction.

Published in:

Journal of Computational Chemistry, 2013, v. 34, n. 27, p. 2360, doi. 10.1002/jcc.23398

By:

Velez‐Vega, Camilo;
Gilson, Michael K.

Publication type:

Article

Efficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methods.

Published in:

Journal of Computational Chemistry, 2008, v. 29, n. 10, p. 1605, doi. 10.1002/jcc.20919

By:

Hnizdo, Vladimir;
Tan, Jun;
Killian, Benjamin J.;
Gilson, Michael K.

Publication type:

Article

Tork: Conformational analysis method for molecules and complexes.

Published in:

Journal of Computational Chemistry, 2003, v. 24, n. 16, p. 1987

By:

Chia-En Chang;
Michael K. Gilson

Publication type:

Article

Enhanced docking with the mining minima optimizer: Acceleration and side-chain flexibility.

Published in:

Journal of Computational Chemistry, 2002, v. 23, n. 16, p. 1656, doi. 10.1002/jcc.10168

By:

Kairys, Visvaldas;
Gilson, Michael K.

Publication type:

Article

Accelerated Poisson-Boltzmann calculations for static and dynamic systems.

Published in:

Journal of Computational Chemistry, 2002, v. 23, n. 13, p. 1244, doi. 10.1002/jcc.10120

By:

Luo, Ray;
David, Laurent;
Gilson, Michael K.

Publication type:

Article

Comparison of generalized born and poisson models: Energetics and dynamics of HIV protease.

Published in:

Journal of Computational Chemistry, 2000, v. 21, n. 4, p. 295, doi. 10.1002/(SICI)1096-987X(200003)21:4<295::AID-JCC5>3.0.CO;2-8

By:

David, Laurent;
Luo, Ray;
Gilson, Michael K.

Publication type:

Article

Thermodynamic linkage between the binding of protons and inhibitors to HIV-1 protease.

Published in:

Protein Science: A Publication of the Protein Society, 1999, v. 8, n. 1, p. 180, doi. 10.1110/ps.8.1.180

By:

Trylska, Joanna;
Antosiewicz, Jan;
Geller, Maciej;
Hodge, C. Nicholas;
Klabe, Ronald M.;
Head, Martha S.;
Gilson, Michael K.

Publication type:

Article

Evaluation of the substrate envelope hypothesis for inhibitors of HIV-1 protease.

Published in:

Proteins, 2007, v. 68, n. 2, p. 561, doi. 10.1002/prot.21431

By:

Chellappan, Sripriya;
Kairys, Visvaldas;
Fernandes, Miguel X.;
Schiffer, Celia;
Gilson, Michael K.

Publication type:

Article

The Carmaphycins: New Proteasome Inhibitors Exhibiting an α,β-Epoxyketone Warhead from a Marine Cyanobacterium.

Published in:

ChemBioChem, 2012, v. 13, n. 6, p. 810, doi. 10.1002/cbic.201200007

By:

Pereira, Alban R.;
Kale, Andrew J.;
Fenley, Andrew T.;
Byrum, Tara;
Debonsi, Hosana M.;
Gilson, Michael K.;
Valeriote, Frederick A.;
Moore, Bradley S.;
Gerwick, William H.

Publication type:

Article

Data-driven analysis of the number of Lennard–Jones types needed in a force field.

Published in:

Communications Chemistry, 2020, v. 3, n. 1, p. 1, doi. 10.1038/s42004-020-00395-w

By:

Schauperl, Michael;
Kantonen, Sophie M;
Wang, Lee-Ping;
Gilson, Michael K

Publication type:

Article

Non-bonded force field model with advanced restrained electrostatic potential charges (RESP2).

Published in:

Communications Chemistry, 2020, v. 3, n. 1, p. 1, doi. 10.1038/s42004-020-0291-4

By:

Schauperl, Michael;
Nerenberg, Paul S.;
Jang, Hyesu;
Wang, Lee-Ping;
Bayly, Christopher I.;
Mobley, David L.;
Gilson, Michael K.

Publication type:

Article

A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site.

Published in:

PLoS ONE, 2019, v. 14, n. 7, p. 1, doi. 10.1371/journal.pone.0219473

By:

Nguyen, Crystal;
Yamazaki, Takeshi;
Kovalenko, Andriy;
Case, David A.;
Gilson, Michael K.;
Kurtzman, Tom;
Luchko, Tyler

Publication type:

Article

BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data.

Published in:

Nucleic Acids Research, 2025, v. 53, n. D1, p. D1633, doi. 10.1093/nar/gkae1075

By:

Liu, Tiqing;
Hwang, Linda;
Burley, Stephen K;
Nitsche, Carmen I;
Southan, Christopher;
Walters, W Patrick;
Gilson, Michael K

Publication type:

Article

BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 1, p. D1045, doi. 10.1093/nar/gkv1072

By:

Gilson, Michael K.;
Tiqing Liu;
Baitaluk, Michael;
Nicola, George;
Hwang, Linda;
Chong, Jenny

Publication type:

Article

Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-05406-y

By:

Chen, Shin-Fu;
Huang, Nan-Lan;
Lin, Jung-Hsin;
Wu, Chyuan-Chuan;
Wang, Ying-Ren;
Yu, Yu-Jen;
Gilson, Michael K.;
Chan, Nei-Li

Publication type:

Article

Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST.

Published in:

Journal of Computational Chemistry, 2016, v. 37, n. 21, p. 2029, doi. 10.1002/jcc.24417

By:

Ramsey, Steven;
Nguyen, Crystal;
Salomon‐Ferrer, Romelia;
Walker, Ross C.;
Gilson, Michael K.;
Kurtzman, Tom

Publication type:

Article

Toward the Design of Mutation-Resistant Enzyme Inhibitors: Further Evaluation of the Substrate Envelope Hypothesis.

Published in:

Chemical Biology & Drug Design, 2009, v. 74, n. 3, p. 234, doi. 10.1111/j.1747-0285.2009.00851.x

By:

Kairys, Visvaldas;
Gilson, Michael K.;
Lather, Viney;
Schiffer, Celia A.;
Fernandes, Miguel X.

Publication type:

Article

Design of Mutation-resistant HIV Protease Inhibitors with the Substrate Envelope Hypothesis.

Published in:

Chemical Biology & Drug Design, 2007, v. 69, n. 5, p. 298, doi. 10.1111/j.1747-0285.2007.00514.x

By:

Chellappan, Sripriya;
Kiran Kumar Reddy, G. S.;
Ali, Akbar;
Nalam, Madhavi N. L.;
Anjum, Saima Ghafoor;
Cao, Hong;
Kairys, Visvaldas;
Fernandes, Miguel X.;
Altman, Michael D.;
Tidor, Bruce;
Rana, Tariq M.;
Schiffer, Celia A.;
Gilson, Michael K.

Publication type:

Article

Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo.

Published in:

Journal of Computer-Aided Molecular Design, 2021, v. 35, n. 2, p. 167, doi. 10.1007/s10822-020-00344-8

By:

Bergazin, Teresa Danielle;
Ben-Shalom, Ido Y.;
Lim, Nathan M.;
Gill, Sam C.;
Gilson, Michael K.;
Mobley, David L.

Publication type:

Article

The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations.

Published in:

Journal of Computer-Aided Molecular Design, 2020, v. 34, n. 5, p. 601, doi. 10.1007/s10822-020-00290-5

By:

Rizzi, Andrea;
Jensen, Travis;
Slochower, David R.;
Aldeghi, Matteo;
Gapsys, Vytautas;
Ntekoumes, Dimitris;
Bosisio, Stefano;
Papadourakis, Michail;
Henriksen, Niel M.;
de Groot, Bert L.;
Cournia, Zoe;
Dickson, Alex;
Michel, Julien;
Gilson, Michael K.;
Shirts, Michael R.;
Mobley, David L.;
Chodera, John D.

Publication type:

Article

Drug Design Data Resource, Grand Challenge 4, second of two issues.

Published in:

2020

By:

Gilson, Michael K.;
Amaro, Rommie E.

Publication type:

Editorial

D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies.

Published in:

Journal of Computer-Aided Molecular Design, 2020, v. 34, n. 2, p. 99, doi. 10.1007/s10822-020-00289-y

By:

Parks, Conor D.;
Gaieb, Zied;
Chiu, Michael;
Yang, Huanwang;
Shao, Chenghua;
Walters, W. Patrick;
Jansen, Johanna M.;
McGaughey, Georgia;
Lewis, Richard A.;
Bembenek, Scott D.;
Ameriks, Michael K.;
Mirzadegan, Tara;
Burley, Stephen K.;
Amaro, Rommie E.;
Gilson, Michael K.

Publication type:

Article

This issue: Drug Design Data Resource Grand Challenge 4, first of two issues.

Published in:

2019

By:

Gilson, Michael K.

Publication type:

Editorial

Automation of absolute protein-ligand binding free energy calculations for docking refinement and compound evaluation.

Published in:

Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-020-80769-1

By:

Heinzelmann, Germano;
Gilson, Michael K.

Publication type:

Article

Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME.

Published in:

Database: The Journal of Biological Databases & Curation, 2015, v. 2015, p. 1, doi. 10.1093/database/bav087

By:

Nicola, George;
Berthold, Michael R.;
Hedrick, Michael P.;
Gilson, Michael K.

Publication type:

Article

Calculation and Visualization of Atomistic Mechanical Stresses in Nanomaterials and Biomolecules.

Published in:

PLoS ONE, 2014, v. 9, n. 12, p. 1, doi. 10.1371/journal.pone.0113119

By:

Fenley, Andrew T.;
Muddana, Hari S.;
Gilson, Michael K.

Publication type:

Article

The dielectric constant of a folded protein.

Published in:

Biopolymers, 1986, v. 25, n. 11, p. 2097, doi. 10.1002/bip.360251106

By:

Gilson, Michael K.;
Honig, Barry H.

Publication type:

Article

Discovering de novo peptide substrates for enzymes using machine learning.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-07717-6

By:

Tallorin, Lorillee;
Wang, JiaLei;
Kim, Woojoo E.;
Sahu, Swagat;
Kosa, Nicolas M.;
Yang, Pu;
Thompson, Matthew;
Gilson, Michael K.;
Frazier, Peter I.;
Burkart, Michael D.;
Gianneschi, Nathan C.

Publication type:

Article