Michael K. Gilson - Publications

Affiliations: 
1994-2009 Molecular and Cell Biology University of Maryland, College Park, College Park, MD 
 2010- Skaggs School of Pharmacy and Pharmaceutical Sciences University of California, San Diego, La Jolla, CA 
Area:
Statistical mechanics, molecular modeling, computer-aided drug design, chemical informatics
Website:
http://gilson.cloud.ucsd.edu/

165 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Heinzelmann G, Gilson MK. Automation of absolute protein-ligand binding free energy calculations for docking refinement and compound evaluation. Scientific Reports. 11: 1116. PMID 33441879 DOI: 10.1038/s41598-020-80769-1  0.383
2020 Ben-Shalom IY, Lin Z, Radak BK, Lin C, Sherman W, Gilson MK. Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations. Journal of Chemical Theory and Computation. PMID 33206520 DOI: 10.1021/acs.jctc.0c00785  0.439
2020 Rizzi A, Jensen T, Slochower DR, Aldeghi M, Gapsys V, Ntekoumes D, Bosisio S, Papadourakis M, Henriksen NM, de Groot BL, Cournia Z, Dickson A, Michel J, Gilson MK, Shirts MR, et al. The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. Journal of Computer-Aided Molecular Design. PMID 31984465 DOI: 10.1007/S10822-020-00290-5  0.816
2020 Parks CD, Gaieb Z, Chiu M, Yang H, Shao C, Walters WP, Jansen JM, McGaughey G, Lewis RA, Bembenek SD, Ameriks MK, Mirzadegan T, Burley SK, Amaro RE, Gilson MK. D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. Journal of Computer-Aided Molecular Design. PMID 31974851 DOI: 10.1007/S10822-020-00289-Y  0.401
2020 Kantonen SM, Muddana HS, Schauperl M, Henriksen NM, Wang LP, Gilson MK. Data-Driven Mapping of Gas-Phase Quantum Calculations to General Force Field Lennard-Jones Parameters. Journal of Chemical Theory and Computation. PMID 31917572 DOI: 10.1021/Acs.Jctc.9B00713  0.74
2020 Ben-Shalom IY, Lin C, Kurtzman T, Walker R, Gilson MK. Equilibration of Buried Water Molecules to Enhance Protein-Ligand Binding Free Energy Calculations Biophysical Journal. 118: 144a. DOI: 10.1016/J.Bpj.2019.11.908  0.476
2019 Slochower DR, Henriksen NM, Wang LP, Chodera JD, Mobley DL, Gilson M. Binding thermodynamics of host-guest systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative. Journal of Chemical Theory and Computation. PMID 31603667 DOI: 10.1021/Acs.Jctc.9B00748  0.82
2019 Callmann CE, LeGuyader CLM, Burton ST, Thompson MP, Hennis R, Barback C, Henriksen NM, Chan WC, Jaremko MJ, Yang J, Garcia A, Burkart MD, Gilson MK, Momper JD, Bertin PA, et al. Antitumor Activity of 1,18-Octadecanedioic Acid-Paclitaxel Complexed with Human Serum Albumin. Journal of the American Chemical Society. PMID 31317744 DOI: 10.1021/Jacs.9B04272  0.718
2019 Nguyen C, Yamazaki T, Kovalenko A, Case DA, Gilson MK, Kurtzman T, Luchko T. A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site. Plos One. 14: e0219473. PMID 31291328 DOI: 10.1371/Journal.Pone.0219473  0.679
2019 Wagner JR, Churas CP, Liu S, Swift RV, Chiu M, Shao C, Feher VA, Burley SK, Gilson MK, Amaro RE. Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking. Structure (London, England : 1993). PMID 31257108 DOI: 10.1016/J.Str.2019.05.012  0.358
2019 Ben-Shalom IY, Lin C, Kurtzman T, Walker RC, Gilson MK. Simulating Water Exchange to Buried Binding Sites. Journal of Chemical Theory and Computation. PMID 30835999 DOI: 10.1021/Acs.Jctc.8B01284  0.431
2019 Gaieb Z, Parks CD, Chiu M, Yang H, Shao C, Walters WP, Lambert MH, Nevins N, Bembenek SD, Ameriks MK, Mirzadegan T, Burley SK, Amaro RE, Gilson MK. D3R Grand Challenge 3: blind prediction of protein-ligand poses and affinity rankings. Journal of Computer-Aided Molecular Design. PMID 30632055 DOI: 10.1007/S10822-018-0180-4  0.351
2018 Zanette C, Bannan CC, Bayly CI, Fass J, Gilson MK, Shirts MR, Chodera JD, Mobley DL. Toward learned chemical perception of force field typing rules. Journal of Chemical Theory and Computation. PMID 30512951 DOI: 10.1021/Acs.Jctc.8B00821  0.337
2018 Rizzi A, Murkli S, McNeill JN, Yao W, Sullivan M, Gilson MK, Chiu MW, Isaacs L, Gibb BC, Mobley DL, Chodera JD. Overview of the SAMPL6 host-guest binding affinity prediction challenge. Journal of Computer-Aided Molecular Design. PMID 30415285 DOI: 10.1007/S10822-018-0170-6  0.483
2018 Li A, Gilson MK. Protein-ligand binding enthalpies from near-millisecond simulations: Analysis of a preorganization paradox. The Journal of Chemical Physics. 149: 072311. PMID 30134726 DOI: 10.1063/1.5027439  0.471
2018 Yin J, Henriksen NM, Muddana HS, Gilson MK. Bind3P: Optimization of a Water Model Based on Host-Guest Binding Data. Journal of Chemical Theory and Computation. PMID 29874074 DOI: 10.1021/Acs.Jctc.8B00318  0.786
2018 Slochower DR, Gilson MK. Motor-like Properties of Nonmotor Enzymes. Biophysical Journal. 114: 2174-2179. PMID 29742410 DOI: 10.1016/J.Bpj.2018.02.008  0.753
2018 Kellett K, Kantonen SA, Duggan BM, Gilson MK. Toward Expanded Diversity of Host–Guest Interactions via Synthesis and Characterization of Cyclodextrin Derivatives Journal of Solution Chemistry. 47: 1597-1608. DOI: 10.1007/S10953-018-0769-1  0.356
2017 Kantonen SA, Henriksen NM, Gilson MK. Accounting for apparent deviations between calorimetric and van't Hoff enthalpies. Biochimica Et Biophysica Acta. PMID 29221984 DOI: 10.1016/J.Bbagen.2017.11.020  0.754
2017 Gaieb Z, Liu S, Gathiaka S, Chiu M, Yang H, Shao C, Feher VA, Walters WP, Kuhn B, Rudolph MG, Burley SK, Gilson MK, Amaro RE. D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. Journal of Computer-Aided Molecular Design. PMID 29204945 DOI: 10.1007/S10822-017-0088-4  0.404
2017 Haider K, Cruz A, Ramsey S, Gilson MK, Kurtzman T. 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. PMID 29161510 DOI: 10.1021/Acs.Jctc.7B00592  0.409
2017 Assaf KI, Florea M, Antony J, Henriksen NM, Yin J, Hansen A, Qu ZW, Sure R, Klapstein D, Gilson MK, Grimme S, Nau WM. The 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. PMID 29140701 DOI: 10.1021/Acs.Jpcb.7B09175  0.796
2017 Balius TE, Fischer M, Stein RM, Adler TB, Nguyen CN, Cruz A, Gilson MK, Kurtzman T, Shoichet BK. Testing inhomogeneous solvation theory in structure-based ligand discovery. Proceedings of the National Academy of Sciences of the United States of America. PMID 28760952 DOI: 10.1073/Pnas.1703287114  0.705
2017 Henriksen NM, Gilson MK. 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. PMID 28696692 DOI: 10.1021/Acs.Jctc.7B00359  0.794
2017 Heinzelmann G, Henriksen NM, Gilson MK. Attach-pull-release calculations of ligand binding and conformational changes on the first BRD4 bromodomain. Journal of Chemical Theory and Computation. PMID 28564537 DOI: 10.1021/Acs.Jctc.7B00275  0.794
2017 Reany O, Li A, Yefet M, Gilson MK, Keinan E. Attractive interactions between heteroallenes and the cucurbituril portal. Journal of the American Chemical Society. PMID 28532152 DOI: 10.1021/Jacs.6B13005  0.319
2017 Mobley DL, Gilson MK. Predicting Binding Free Energies. Annual Review of Biophysics. PMID 28399632 DOI: 10.1146/Annurev-Biophys-070816-033654  0.483
2017 Lee KS, Henriksen NM, Ng CJ, Yang J, Jia W, Morisseau C, Andaya A, Gilson MK, Hammock BD. Probing the orientation of inhibitor and epoxy-eicosatrienoic acid binding in the active site of soluble epoxide hydrolase. Archives of Biochemistry and Biophysics. 613: 1-11. PMID 27983948 DOI: 10.1016/J.Abb.2016.10.017  0.744
2017 Kantonen SA, Henriksen NM, Gilson MK. Evaluation and Minimization of Uncertainty in ITC Binding Measurements: Heat Error, Concentration Error, Saturation, and Stoichiometry. Biochimica Et Biophysica Acta. 1861: 485-498. PMID 27599357 DOI: 10.1016/J.Bbagen.2016.09.002  0.764
2016 Shirts MR, Klein C, Swails JM, Yin J, Gilson MK, Mobley DL, Case DA, Zhong ED. Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. Journal of Computer-Aided Molecular Design. PMID 27787702 DOI: 10.1007/S10822-016-9977-1  0.369
2016 Gathiaka S, Liu S, Chiu M, Yang H, Stuckey JA, Kang YN, Delproposto J, Kubish G, Dunbar JB, Carlson HA, Burley SK, Walters WP, Amaro RE, Feher VA, Gilson MK. D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions. Journal of Computer-Aided Molecular Design. 30: 651-668. PMID 27696240 DOI: 10.1007/S10822-016-9946-8  0.64
2016 Bannan CC, Burley KH, Chiu M, Shirts MR, Gilson MK, Mobley DL. Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge. Journal of Computer-Aided Molecular Design. 30: 927-944. PMID 27677750 DOI: 10.1007/S10822-016-9954-8  0.36
2016 Yin J, Henriksen NM, Slochower DR, Shirts MR, Chiu MW, Mobley DL, Gilson MK. Overview of the SAMPL5 host-guest challenge: Are we doing better? Journal of Computer-Aided Molecular Design. PMID 27658802 DOI: 10.1007/S10822-016-9974-4  0.81
2016 Yin J, Henriksen NM, Slochower DR, Gilson MK. The SAMPL5 host-guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method. Journal of Computer-Aided Molecular Design. PMID 27638809 DOI: 10.1007/S10822-016-9970-8  0.831
2016 Ramsey S, Nguyen C, Salomon-Ferrer R, Walker RC, Gilson MK, Kurtzman T. Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST. Journal of Computational Chemistry. 37: 2029-37. PMID 27317094 DOI: 10.1002/Jcc.24417  0.66
2016 Machan CW, Yin J, Chabolla SA, Gilson MK, Kubiak CP. Improving the Efficiency and Activity of Electrocatalysts for the Reduction of CO2 through Supramolecular Assembly with Amino Acid-Modified Ligands. Journal of the American Chemical Society. 138: 8184-93. PMID 27258781 DOI: 10.1021/Jacs.6B03774  0.303
2016 Li A, Voronin A, Fenley AT, Gilson MK. Evaluation of Representations and Response Models for Polarizable Force Fields. The Journal of Physical Chemistry. B. 120: 8668-84. PMID 27248842 DOI: 10.1021/Acs.Jpcb.6B03392  0.326
2016 Haider K, Wickstrom L, Ramsey S, Gilson MK, Kurtzman T. Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces. The Journal of Physical Chemistry. B. 120: 8743-56. PMID 27169482 DOI: 10.1021/Acs.Jpcb.6B01094  0.354
2016 Nguyen CN, Kurtzman T, Gilson MK. Spatial Decomposition of Translational Water-Water Correlation Entropy in Binding Pockets. Journal of Chemical Theory and Computation. 12: 414-29. PMID 26636620 DOI: 10.1021/Acs.Jctc.5B00939  0.671
2016 Gilson MK, Liu T, Baitaluk M, Nicola G, Hwang L, Chong J. BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology. Nucleic Acids Research. 44: D1045-53. PMID 26481362 DOI: 10.1093/Nar/Gkv1072  0.357
2016 Wickstrom L, Deng N, He P, Mentes A, Nguyen C, Gilson MK, Kurtzman T, Gallicchio E, Levy RM. Parameterization of an effective potential for protein-ligand binding from host-guest affinity data. Journal of Molecular Recognition : Jmr. 29: 10-21. PMID 26256816 DOI: 10.1002/Jmr.2489  0.745
2015 Gao K, Yin J, Henriksen NM, Fenley AT, Gilson MK. Binding enthalpy calculations for a neutral host-guest pair yield widely divergent salt effects across water models. Journal of Chemical Theory and Computation. 11: 4555-64. PMID 26574247 DOI: 10.1021/Acs.Jctc.5B00676  0.783
2015 Henriksen NM, Fenley AT, Gilson MK. Computational Calorimetry: High-Precision Calculation of Host-Guest Binding Thermodynamics. Journal of Chemical Theory and Computation. 11: 4377-94. PMID 26523125 DOI: 10.1021/Acs.Jctc.5B00405  0.806
2015 Nicola G, Berthold MR, Hedrick MP, Gilson MK. Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME. Database : the Journal of Biological Databases and Curation. 2015. PMID 26384374 DOI: 10.1093/Database/Bav087  0.311
2015 Yin J, Fenley AT, Henriksen NM, Gilson MK. Toward Improved Force-Field Accuracy through Sensitivity Analysis of Host-Guest Binding Thermodynamics. The Journal of Physical Chemistry. B. 119: 10145-55. PMID 26181208 DOI: 10.1021/Acs.Jpcb.5B04262  0.788
2015 Yin J, Fenley AT, Henriksen NM, Gilson MK. Toward Improved Force-Field Accuracy through Sensitivity Analysis of Host-Guest Binding Thermodynamics Journal of Physical Chemistry B. 119: 10145-10155. DOI: 10.1021/acs.jpcb.5b04262  0.744
2015 Gao K, Yin J, Henriksen NM, Fenley AT, Gilson MK. Binding Enthalpy Calculations for a Neutral Host-Guest Pair Yield Widely Divergent Salt Effects across Water Models Journal of Chemical Theory and Computation. 11: 4555-4564. DOI: 10.1021/acs.jctc.5b00676  0.755
2015 Wickstrom L, Deng N, He P, Mentes A, Nguyen C, Gilson MK, Kurtzman T, Gallicchio E, Levy RM. Parameterization of an effective potential for protein-ligand binding from host-guest affinity data Journal of Molecular Recognition. DOI: 10.1002/jmr.2489  0.67
2014 Fenley AT, Henriksen NM, Muddana HS, Gilson MK. Bridging Calorimetry and Simulation through Precise Calculations of Cucurbituril-Guest Binding Enthalpies. Journal of Chemical Theory and Computation. 10: 4069-4078. PMID 25221445 DOI: 10.1021/Ct5004109  0.796
2014 Nguyen CN, Cruz A, Gilson MK, Kurtzman T. Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa. Journal of Chemical Theory and Computation. 10: 2769-2780. PMID 25018673 DOI: 10.1021/Ct401110X  0.675
2014 Li A, Muddana HS, Gilson MK. Quantum Mechanical Calculation of Noncovalent Interactions: A Large-Scale Evaluation of PMx, DFT, and SAPT Approaches. Journal of Chemical Theory and Computation. 10: 1563-1575. PMID 24803867 DOI: 10.1021/Ct401111C  0.424
2014 Fenley AT, Killian BJ, Hnizdo V, Fedorowicz A, Sharp DS, Gilson MK. Correlation as a determinant of configurational entropy in supramolecular and protein systems. The Journal of Physical Chemistry. B. 118: 6447-55. PMID 24702693 DOI: 10.1021/Jp411588B  0.38
2014 Muddana HS, Fenley AT, Mobley DL, Gilson MK. The SAMPL4 host-guest blind prediction challenge: an overview. Journal of Computer-Aided Molecular Design. 28: 305-17. PMID 24599514 DOI: 10.1007/S10822-014-9735-1  0.473
2014 Muddana HS, Yin J, Sapra NV, Fenley AT, Gilson MK. Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method. Journal of Computer-Aided Molecular Design. 28: 463-74. PMID 24510191 DOI: 10.1007/S10822-014-9726-2  0.476
2014 Muddana HS, Sapra NV, Fenley AT, Gilson MK. The SAMPL4 hydration challenge: evaluation of partial charge sets with explicit-water molecular dynamics simulations. Journal of Computer-Aided Molecular Design. 28: 277-87. PMID 24477800 DOI: 10.1007/S10822-014-9714-6  0.401
2014 Nguyen CN, Cruz A, Gilson MK, Kurtzman T. Thermodynamics of water in an enzyme active site: Grid-based hydration analysis of coagulation factor xa Journal of Chemical Theory and Computation. 10: 2769-2780. DOI: 10.1021/ct401110x  0.596
2014 Gilson MK, Fenley AT, Muddana H. Bridging Simulations and Calorimetry: Computational Studies of Binding Thermodynamics and Entropy-Enthalpy Transduction Biophysical Journal. 106: 658a. DOI: 10.1016/J.Bpj.2013.11.3646  0.496
2013 Velez-Vega C, Gilson MK. Overcoming dissipation in the calculation of standard binding free energies by ligand extraction. Journal of Computational Chemistry. 34: 2360-71. PMID 24038118 DOI: 10.1002/Jcc.23398  0.495
2013 Muddana HS, Sapra NV, Fenley AT, Gilson MK. The electrostatic response of water to neutral polar solutes: implications for continuum solvent modeling. The Journal of Chemical Physics. 138: 224504. PMID 23781802 DOI: 10.1063/1.4808376  0.366
2013 Muddana HS, Fenley AT, Gilson MK. Atomic Stress Propagation Reveals Allosteric Pathways in Proteins Biophysical Journal. 104: 212a. DOI: 10.1016/J.Bpj.2012.11.1197  0.392
2012 Shen Y, Gilson MK, Tidor B. Charge Optimization Theory for Induced-Fit Ligands. Journal of Chemical Theory and Computation. 8: 4580-4592. PMID 23162383 DOI: 10.1021/Ct200931C  0.436
2012 Fenley AT, Muddana HS, Gilson MK. Entropy-enthalpy transduction caused by conformational shifts can obscure the forces driving protein-ligand binding. Proceedings of the National Academy of Sciences of the United States of America. 109: 20006-11. PMID 23150595 DOI: 10.1073/Pnas.1213180109  0.47
2012 Nguyen CN, Young TK, Gilson MK. Grid inhomogeneous solvation theory: hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril. The Journal of Chemical Physics. 137: 044101. PMID 22852591 DOI: 10.1063/1.4733951  0.71
2012 Velez-Vega C, Gilson MK. Force and Stress along Simulated Dissociation Pathways of Cucurbituril-Guest Systems. Journal of Chemical Theory and Computation. 8: 966-976. PMID 22754402 DOI: 10.1021/Ct2006902  0.396
2012 Muddana HS, Gilson MK. Calculation of Host-Guest Binding Affinities Using a Quantum-Mechanical Energy Model. Journal of Chemical Theory and Computation. 8: 2023-2033. PMID 22737045 DOI: 10.1021/Ct3002738  0.5
2012 Nicola G, Liu T, Gilson MK. Public domain databases for medicinal chemistry. Journal of Medicinal Chemistry. 55: 6987-7002. PMID 22731701 DOI: 10.1021/Jm300501T  0.335
2012 Forrey C, Douglas JF, Gilson MK. The Fundamental Role of Flexibility on the Strength of Molecular Binding. Soft Matter. 8: 6385-6392. PMID 22707976 DOI: 10.1039/C2Sm25160D  0.476
2012 Muddana HS, Varnado CD, Bielawski CW, Urbach AR, Isaacs L, Geballe MT, Gilson MK. Blind prediction of host-guest binding affinities: a new SAMPL3 challenge. Journal of Computer-Aided Molecular Design. 26: 475-87. PMID 22366955 DOI: 10.1007/S10822-012-9554-1  0.482
2012 Muddana HS, Gilson MK. Prediction of SAMPL3 host-guest binding affinities: evaluating the accuracy of generalized force-fields. Journal of Computer-Aided Molecular Design. 26: 517-25. PMID 22274835 DOI: 10.1007/S10822-012-9544-3  0.451
2012 Nguyen CN, Young TK, Gilson MK. Erratum: “Grid inhomogeneous solvation theory: Hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril” [J. Chem. Phys. 137, 044101 (2012)] The Journal of Chemical Physics. 137: 149901. DOI: 10.1063/1.4751113  0.612
2012 Nicola G, Liu T, Hwang L, Gilson M. BindingDB: A Protein-Ligand Database for Drug Discovery Biophysical Journal. 102: 61a. DOI: 10.1016/J.Bpj.2011.11.365  0.397
2012 Fenley AT, Gilson MK. Entropic Insights from Millisecond Protein Simulations Biophysical Journal. 102: 448a. DOI: 10.1016/J.Bpj.2011.11.2458  0.388
2011 Orchard S, Al-Lazikani B, Bryant S, Clark D, Calder E, Dix I, Engkvist O, Forster M, Gaulton A, Gilson M, Glen R, Grigorov M, Hammond-Kosack K, Harland L, Hopkins A, et al. Minimum information about a bioactive entity (MIABE). Nature Reviews. Drug Discovery. 10: 661-9. PMID 21878981 DOI: 10.1038/Nrd3503  0.301
2011 Somani S, Gilson MK. Accelerated convergence of molecular free energy via superposition approximation-based reference states. The Journal of Chemical Physics. 134: 134107. PMID 21476743 DOI: 10.1063/1.3571441  0.642
2011 Moghaddam S, Yang C, Rekharsky M, Ko YH, Kim K, Inoue Y, Gilson MK. New ultrahigh affinity host-guest complexes of cucurbit[7]uril with bicyclo[2.2.2]octane and adamantane guests: thermodynamic analysis and evaluation of M2 affinity calculations. Journal of the American Chemical Society. 133: 3570-81. PMID 21341773 DOI: 10.1021/Ja109904U  0.461
2010 Gilson MK. Stress Analysis at the Molecular Level: A Forced Cucurbituril-Guest Dissociation Pathway. Journal of Chemical Theory and Computation. 6: 637-646. PMID 23794959 DOI: 10.1021/Ct900668K  0.4
2010 Chen W, Gilson MK, Webb SP, Potter MJ. Modeling Protein-Ligand Binding by Mining Minima. Journal of Chemical Theory and Computation. 6: 3540-3557. PMID 22639555 DOI: 10.1021/Ct100245N  0.525
2010 Gilson MK, Irikura KK. Symmetry numbers for rigid, flexible, and fluxional molecules: theory and applications. The Journal of Physical Chemistry. B. 114: 16304-17. PMID 21141931 DOI: 10.1021/Jp110434S  0.356
2010 Nalam MN, Ali A, Altman MD, Reddy GS, Chellappan S, Kairys V, Ozen A, Cao H, Gilson MK, Tidor B, Rana TM, Schiffer CA. Evaluating the substrate-envelope hypothesis: structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance. Journal of Virology. 84: 5368-78. PMID 20237088 DOI: 10.1128/Jvi.02531-09  0.581
2009 Zhou HX, Gilson MK. Theory of free energy and entropy in noncovalent binding. Chemical Reviews. 109: 4092-107. PMID 19588959 DOI: 10.1021/Cr800551W  0.505
2009 Killian BJ, Kravitz JY, Somani S, Dasgupta P, Pang YP, Gilson MK. Configurational entropy in protein-peptide binding: computational study of Tsg101 ubiquitin E2 variant domain with an HIV-derived PTAP nonapeptide. Journal of Molecular Biology. 389: 315-35. PMID 19362095 DOI: 10.1016/J.Jmb.2009.04.003  0.646
2009 Somani S, Killian BJ, Gilson MK. Sampling conformations in high dimensions using low-dimensional distribution functions. The Journal of Chemical Physics. 130: 134102. PMID 19355712 DOI: 10.1063/1.3088434  0.583
2009 Boda D, Valiskó M, Henderson D, Gillespie D, Eisenberg B, Gilson MK. Ions and inhibitors in the binding site of HIV protease: comparison of Monte Carlo simulations and the linearized Poisson-Boltzmann theory. Biophysical Journal. 96: 1293-306. PMID 19217848 DOI: 10.1016/J.Bpj.2008.10.059  0.36
2009 Jorissen RN, Reddy GS, Ali A, Altman MD, Chellappan S, Anjum SG, Tidor B, Schiffer CA, Rana TM, Gilson MK. Additivity in the analysis and design of HIV protease inhibitors. Journal of Medicinal Chemistry. 52: 737-54. PMID 19193159 DOI: 10.1021/Jm8009525  0.592
2009 Moghaddam S, Inoue Y, Gilson MK. Host-guest complexes with protein-ligand-like affinities: computational analysis and design. Journal of the American Chemical Society. 131: 4012-21. PMID 19133781 DOI: 10.1021/Ja808175M  0.466
2008 Altman MD, Ali A, Reddy GS, Nalam MN, Anjum SG, Cao H, Chellappan S, Kairys V, Fernandes MX, Gilson MK, Schiffer CA, Rana TM, Tidor B. HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants. Journal of the American Chemical Society. 130: 6099-113. PMID 18412349 DOI: 10.1021/Ja076558P  0.592
2008 Hnizdo V, Tan J, Killian BJ, Gilson MK. Efficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methods. Journal of Computational Chemistry. 29: 1605-14. PMID 18293293 DOI: 10.1002/Jcc.20919  0.386
2007 Rekharsky MV, Mori T, Yang C, Ko YH, Selvapalam N, Kim H, Sobransingh D, Kaifer AE, Liu S, Isaacs L, Chen W, Moghaddam S, Gilson MK, Kim K, Inoue Y. A synthetic host-guest system achieves avidin-biotin affinity by overcoming enthalpy-entropy compensation. Proceedings of the National Academy of Sciences of the United States of America. 104: 20737-42. PMID 18093926 DOI: 10.1073/Pnas.0706407105  0.329
2007 Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, ... ... Gilson M, et al. Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. Bmc Biology. 5: 44. PMID 17925023 DOI: 10.1186/1741-7007-5-44  0.318
2007 Killian BJ, Yundenfreund Kravitz J, Gilson MK. Extraction of configurational entropy from molecular simulations via an expansion approximation. The Journal of Chemical Physics. 127: 024107. PMID 17640119 DOI: 10.1063/1.2746329  0.389
2007 Chellappan S, Kiran Kumar Reddy GS, Ali A, Nalam MN, Anjum SG, Cao H, Kairys V, Fernandes MX, Altman MD, Tidor B, Rana TM, Schiffer CA, Gilson MK. Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis. Chemical Biology & Drug Design. 69: 298-313. PMID 17539822 DOI: 10.1111/J.1747-0285.2007.00514.X  0.551
2007 Chellappan S, Kairys V, Fernandes MX, Schiffer C, Gilson MK. Evaluation of the substrate envelope hypothesis for inhibitors of HIV-1 protease. Proteins. 68: 561-7. PMID 17474129 DOI: 10.1002/Prot.21431  0.569
2007 Chen W, Gilson MK. ConCept: de novo design of synthetic receptors for targeted ligands. Journal of Chemical Information and Modeling. 47: 425-34. PMID 17315861 DOI: 10.1021/Ci600233V  0.332
2007 Chang CE, Chen W, Gilson MK. Ligand configurational entropy and protein binding. Proceedings of the National Academy of Sciences of the United States of America. 104: 1534-9. PMID 17242351 DOI: 10.1073/Pnas.0610494104  0.666
2007 Gilson MK, Zhou HX. Calculation of protein-ligand binding affinities. Annual Review of Biophysics and Biomolecular Structure. 36: 21-42. PMID 17201676 DOI: 10.1146/Annurev.Biophys.36.040306.132550  0.511
2007 Liu T, Lin Y, Wen X, Jorissen RN, Gilson MK. BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Research. 35: D198-201. PMID 17145705 DOI: 10.1093/Nar/Gkl999  0.374
2006 Gilson MK. Sensitivity Analysis and Charge-Optimization for Flexible Ligands:  Applicability to Lead Optimization. Journal of Chemical Theory and Computation. 2: 259-70. PMID 26626513 DOI: 10.1021/Ct050226Y  0.371
2006 Kairys V, Gilson MK, Fernandes MX. Using protein homology models for structure-based studies: Approaches to model refinement Thescientificworldjournal. 6: 1542-1554. PMID 17160340 DOI: 10.1100/Tsw.2006.250  0.311
2006 Chen W, Chang CE, Gilson MK. Concepts in receptor optimization: targeting the RGD peptide. Journal of the American Chemical Society. 128: 4675-84. PMID 16594704 DOI: 10.1021/Ja056600L  0.624
2006 Kairys V, Fernandes MX, Gilson MK. Screening drug-like compounds by docking to homology models: a systematic study. Journal of Chemical Information and Modeling. 46: 365-79. PMID 16426071 DOI: 10.1021/Ci050238C  0.329
2005 Chang CE, Chen W, Gilson MK. Evaluating the Accuracy of the Quasiharmonic Approximation. Journal of Chemical Theory and Computation. 1: 1017-28. PMID 26641917 DOI: 10.1021/Ct0500904  0.613
2005 Jorissen RN, Gilson MK. Virtual screening of molecular databases using a support vector machine. Journal of Chemical Information and Modeling. 45: 549-61. PMID 15921445 DOI: 10.1021/Ci049641U  0.307
2004 Fernandes MX, Kairys V, Gilson MK. Comparing ligand interactions with multiple receptors via serial docking. Journal of Chemical Information and Computer Sciences. 44: 1961-70. PMID 15554665 DOI: 10.1021/Ci049803M  0.365
2004 Chang CE, Gilson MK. Free energy, entropy, and induced fit in host-guest recognition: calculations with the second-generation mining minima algorithm. Journal of the American Chemical Society. 126: 13156-64. PMID 15469315 DOI: 10.1021/Ja047115D  0.665
2004 Chen W, Chang CE, Gilson MK. Calculation of cyclodextrin binding affinities: energy, entropy, and implications for drug design. Biophysical Journal. 87: 3035-49. PMID 15339804 DOI: 10.1529/Biophysj.104.049494  0.672
2004 Chen W, Huang J, Gilson MK. Identification of symmetries in molecules and complexes. Journal of Chemical Information and Computer Sciences. 44: 1301-13. PMID 15272838 DOI: 10.1021/Ci049966A  0.372
2004 Mihailescu M, Gilson MK. On the theory of noncovalent binding. Biophysical Journal. 87: 23-36. PMID 15240441 DOI: 10.1529/Biophysj.103.031682  0.442
2003 Gilson MK, Gilson HS, Potter MJ. Fast assignment of accurate partial atomic charges: an electronegativity equalization method that accounts for alternate resonance forms. Journal of Chemical Information and Computer Sciences. 43: 1982-97. PMID 14632449 DOI: 10.1021/Ci034148O  0.334
2003 Chang CE, Gilson MK. Tork: Conformational analysis method for molecules and complexes. Journal of Computational Chemistry. 24: 1987-98. PMID 14531053 DOI: 10.1002/Jcc.10325  0.6
2003 DeJong ES, Chang CE, Gilson MK, Marino JP. Proflavine acts as a Rev inhibitor by targeting the high-affinity Rev binding site of the Rev responsive element of HIV-1. Biochemistry. 42: 8035-46. PMID 12834355 DOI: 10.1021/Bi034252Z  0.629
2003 Parsons L, Bonander N, Eisenstein E, Gilson M, Kairys V, Orban J. Solution structure and functional ligand screening of HI0719, a highly conserved protein from bacteria to humans in the YjgF/YER057c/UK114 family. Biochemistry. 42: 80-9. PMID 12515541 DOI: 10.1021/Bi020541W  0.367
2003 Chang CE, Potter MJ, Gilson MK. Calculation of molecular configuration integrals Journal of Physical Chemistry B. 107: 1048-1055. DOI: 10.1021/Jp027149C  0.582
2002 Kairys V, Gilson MK. Enhanced docking with the mining minima optimizer: acceleration and side-chain flexibility. Journal of Computational Chemistry. 23: 1656-70. PMID 12395431 DOI: 10.1002/Jcc.10168  0.382
2002 Luo R, David L, Gilson MK. Accelerated Poisson-Boltzmann calculations for static and dynamic systems. Journal of Computational Chemistry. 23: 1244-53. PMID 12210150 DOI: 10.1002/Jcc.10120  0.65
2002 Chen X, Lin Y, Liu M, Gilson MK. The Binding Database: data management and interface design. Bioinformatics (Oxford, England). 18: 130-9. PMID 11836221 DOI: 10.1093/Bioinformatics/18.1.130  0.456
2002 Potter MJ, Gilson MK. Coordinate systems and the calculation of molecular properties Journal of Physical Chemistry A. 106: 563-566. DOI: 10.1021/Jp0135407  0.372
2001 Chen X, Lin Y, Gilson MK. The binding database: Overview and user's guide Biopolymers. 61: 127-141. PMID 11987162 DOI: 10.1002/1097-0282(2002)61:2<127::Aid-Bip10076>3.0.Co;2-N  0.452
2001 Chen X, Liu M, Gilson MK. BindingDB: A web-accessible molecular recognition database Combinatorial Chemistry and High Throughput Screening. 4: 719-725. PMID 11812264 DOI: 10.2174/1386207013330670  0.42
2001 Mardis KL, Luo R, Gilson MK. Interpreting trends in the binding of cyclic ureas to HIV-1 protease Journal of Molecular Biology. 309: 507-517. PMID 11371168 DOI: 10.1006/Jmbi.2001.4668  0.691
2001 David L, Luo R, Gilson MK. Ligand-receptor docking with the Mining Minima optimizer Journal of Computer-Aided Molecular Design. 15: 157-171. PMID 11272702 DOI: 10.1023/A:1008128723048  0.658
2001 Luo R, Gilson HSR, Potter MJ, Gilson MK. The physical basis of nucleic acid base stacking in water Biophysical Journal. 80: 140-148. PMID 11159389 DOI: 10.1016/S0006-3495(01)76001-8  0.611
2000 Mardis K, Luo R, David L, Potter M, Glemza A, Payne G, Gilson MK. Modeling molecular recognition: Theory and application Journal of Biomolecular Structure and Dynamics. 17: 89-94. DOI: 10.1080/07391102.2000.10506608  0.69
2000 Mardis KL, Brune BJ, Vishwanath P, Giorgis B, Payne GF, Gilson MK. Intramolecular versus Intermolecular Hydrogen Bonding in the Adsorption of Aromatic Alcohols onto an Acrylic Ester Sorbent Journal of Physical Chemistry B. 104: 4735-4744. DOI: 10.1021/Jp993531M  0.306
2000 Luo R, Gilson MK. Synthetic adenine receptors: Direct calculation of binding affinity and entropy Journal of the American Chemical Society. 122: 2934-2937. DOI: 10.1021/Ja994034M  0.485
2000 Glemza AJ, Mardis KL, Chaudhry AA, Gilson MK, Payne GF. Competition between intra- and intermolecular hydrogen bonding: Effect on para/ortho adsorptive selectivity for substituted phenols Industrial and Engineering Chemistry Research. 39: 463-472. DOI: 10.1021/Ie990594I  0.347
2000 David L, Luo R, Gilson MK. Comparison of generalized born and poisson models: Energetics and dynamics of HIV protease Journal of Computational Chemistry. 21: 295-309. DOI: 10.1002/(Sici)1096-987X(200003)21:4<295::Aid-Jcc5>3.0.Co;2-8  0.566
2000 David L, Luo R, Gilson MK. Comparison of Generalized Born and Poisson Models: Energetics and Dynamics of HIV Protease Journal of Computational Chemistry. 21: 295-309.  0.315
1999 Luo R, Head MS, Given JA, Gilson MK. Nucleic acid base-pairing and N-methylacetamide self-association in chloroform: Affinity and conformation Biophysical Chemistry. 78: 183-193. PMID 10343387 DOI: 10.1016/S0301-4622(98)00229-4  0.663
1999 Trylska J, Antosiewicz J, Geller M, Hodge N, Klabe RM, Head MS, Gilson MK. Thermodynamic linkage between the binding of protons and inhibitors to HIV-1 protease Protein Science. 8: 180-195. PMID 10210196 DOI: 10.1110/Ps.8.1.180  0.426
1999 Mardis KL, Glemza AJ, Brune BJ, Payne GF, Gilson MK. Differential adsorption of phenol derivatives onto a polymeric sorbent: a combined jylolecular modeling and experimental study Journal of Physical Chemistry B. 103: 9879-9887. DOI: 10.1021/Jp991499Q  0.359
1999 David L, Luo R, Head MS, Gilson MK. Computational Study Of Kni-272, A Potent Inhibitor Of Hiv-1 Protease : On The Mechanism Of Preorganization Journal of Physical Chemistry B. 103: 1031-1044. DOI: 10.1021/Jp983675L  0.638
1999 Luo R, David L, Hung H, Devaney aJ, Gilson MK. Strength of Solvent-Exposed Salt-Bridges† The Journal of Physical Chemistry. 103: 727-736. DOI: 10.1021/Jp982715I  0.648
1998 Given JA, Gilson MK. A hierarchical method for generating low-energy conformers of a protein- ligand complex Proteins: Structure, Function and Genetics. 33: 475-495. PMID 9849934 DOI: 10.1002/(Sici)1097-0134(19981201)33:4<475::Aid-Prot3>3.0.Co;2-B  0.456
1998 Forsyth WR, Gilson MK, Antosiewicz J, Jaren OR, Robertson AD. Theoretical and experimental analysis of ionization equilibria in ovomucoid third domain Biochemistry. 37: 8643-8652. PMID 9628726 DOI: 10.1021/Bi980187V  0.318
1998 Luo R, Head MS, Moult J, Gilson MK. pK(a) shifts in small molecules and HIV protease: Electrostatics and conformation Journal of the American Chemical Society. 120: 6138-6146. DOI: 10.1021/Ja974307I  0.35
1997 Gilson MK, Given JA, Head MS. A new class of models for computing receptor-ligand binding affinities Chemistry and Biology. 4: 87-92. PMID 9190290 DOI: 10.1016/S1074-5521(97)90251-9  0.443
1997 Gilson MK, Given JA, Bush BL, McCammon JA. The statistical-thermodynamic basis for computation of binding affinities: A critical review Biophysical Journal. 72: 1047-1069. PMID 9138555 DOI: 10.1016/S0006-3495(97)78756-3  0.609
1997 Khare D, Alexander P, Antosiewicz J, Bryan P, Gilson M, Orban J. pK(a) measurements from nuclear magnetic resonance for the B1 and B2 immunoglobulin G-binding domains of protein G: Comparison with calculated values for nuclear magnetic resonance and x-ray structures Biochemistry. 36: 3580-3589. PMID 9132009 DOI: 10.1021/Bi9630927  0.315
1997 Luo R, Moult J, Gilson MK. Dielectric screening treatment of electrostatic solvation Journal of Physical Chemistry B. 101: 11226-11236. DOI: 10.1021/Jp9724838  0.401
1997 Head MS, Given JA, Gilson MK. ''Mining minima'': Direct computation of conformational free energy Journal of Physical Chemistry A. 101: 1609-1618. DOI: 10.1021/Jp963817G  0.402
1996 Wlodek ST, Antosiewicz J, McCammon JA, Straatsma TP, Gilson MK, Briggs JM, Humblet C, Sussman JL. Binding of tacrine and 6-chlorotacrine by acetylcholinesterase. Biopolymers. 38: 109-17. PMID 8679940 DOI: 10.1002/(SICI)1097-0282(199601)38:1<109::AID-BIP9>3.0.CO;2-#  0.799
1996 Antosiewicz J, McCammon JA, Gilson MK. The determinants of pKaS in proteins Biochemistry. 35: 7819-7833. PMID 8672483 DOI: 10.1021/bi9601565  0.467
1996 Marrone TJ, Gilson MK, McCammon JA. Comparison of Continuum and Explicit Models of Solvation:  Potentials of Mean Force for Alanine Dipeptide The Journal of Physical Chemistry. 100: 1439-1441. DOI: 10.1021/Jp952835F  0.545
1996 Antosiewicz J, Briggs JM, Elcock AH, Gilson MK, McCammon JA. Computing ionization states of proteins with a detailed charge model Journal of Computational Chemistry. 17: 1633-1644. DOI: 10.1002/(Sici)1096-987X(19961115)17:14<1633::Aid-Jcc5>3.0.Co;2-M  0.66
1996 Antosiewicz J, Briggs JM, Elcock AH, Gilson MK, Mccammon JA. Computing ionization states of proteins with a detailed charge model Journal of Computational Chemistry. 17: 1633-1644.  0.592
1995 Antosiewicz J, Gilson MK, Lee IH, McCammon JA. Acetylcholinesterase: Diffusional encounter rate constants for dumbbell models of ligand Biophysical Journal. 68: 62-68. PMID 7711269 DOI: 10.1016/S0006-3495(95)80159-1  0.474
1995 Antosiewicz J, McCammon JA, Wlodek ST, Gilson MK. Simulation of charge-mutant acetylcholinesterases. Biochemistry. 34: 4211-9. PMID 7703233 DOI: 10.1021/bi00013a009  0.34
1995 Gilson MK. Theory of electrostatic interactions in macromolecules Current Opinion in Structural Biology. 5: 216-223. PMID 7648324 DOI: 10.1016/0959-440X(95)80079-4  0.373
1995 Madura JD, Briggs JM, Wade RC, Davis ME, Luty BA, Ilin A, Antosiewicz J, Gilson MK, Bagheri B, Scott LR, McCammon JA. Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program Computer Physics Communications. 91: 57-95. DOI: 10.1016/0010-4655(95)00043-F  0.647
1995 Gilson MK, McCammon JA, Madura JD. Molecular dynamics simulation with a continuum electrostatic model of the solvent Journal of Computational Chemistry. 16: 1081-1095. DOI: 10.1002/Jcc.540160904  0.685
1994 Antosiewicz J, McCammon JA, Gilson MK. Prediction of pH-dependent properties of proteins Journal of Molecular Biology. 238: 415-436. PMID 8176733 DOI: 10.1006/Jmbi.1994.1301  0.518
1994 Gilson MK, Straatsma TP, McCammon JA, Ripoll DR, Faerman CH, Axelsen PH, Silman I, Sussman JL. Open 'back door' in a molecular dynamics simulation of acetylcholinesterase Science. 263: 1276-1278. PMID 8122110 DOI: 10.1126/science.8122110  0.677
1994 Potter MJ, Gilson MK, McCammon JA. Small molecule pKa prediction with continuum electrostatics calculations Journal of the American Chemical Society. 116: 10298-10299. DOI: 10.1021/Ja00101A059  0.344
1994 Potter MJ, Gilson MK, McCammon JA. Small Molecule pKa Prediction with Continuum Electrostatics Calculations Journal of the American Chemical Society. 116: 10298-10299. DOI: 10.1021/ja00101a059  0.412
1994 Antosiewicz J, Gilson MK, Mccammon JA. Acetylcholinesterase: Effects of Ionic Strength and Dimerization on the Rate Constants Israel Journal of Chemistry. 34: 151-158. DOI: 10.1002/Ijch.199400020  0.488
1993 Gilson MK. Multiple-site titration and molecular modeling: Two rapid methods for computing energies and forces for ionizable groups in proteins Proteins: Structure, Function and Genetics. 15: 266-282. PMID 8456096 DOI: 10.1002/Prot.340150305  0.405
1993 Gilson MK, Davis ME, Luty BA, McCammon JA. Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation The Journal of Physical Chemistry. 97: 3591-3600. DOI: 10.1021/J100116A025  0.497
1991 Gilson MK, Honig B. The inclusion of electrostatic hydration energies in molecular mechanics calculations Journal of Computer-Aided Molecular Design. 5: 5-20. PMID 2072125 DOI: 10.1007/Bf00173467  0.588
1989 Gilson MK, Honig B. Destabilization of an alpha-helix-bundle protein by helix dipoles Proceedings of the National Academy of Sciences of the United States of America. 86: 1524-1528. PMID 2922396 DOI: 10.1073/Pnas.86.5.1524  0.542
1988 Gilson MK, Honig BH. Energetics of charge-charge interactions in proteins. Proteins. 3: 32-52. PMID 3287370 DOI: 10.1002/Prot.340030104  0.556
1988 Gilson MK, Honig B. Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis Proteins. 4: 7-18. PMID 3186692 DOI: 10.1002/Prot.340040104  0.599
1988 Gilson MK, Sharp KA, Honig BH. Calculating the electrostatic potential of molecules in solution: Method and error assessment Journal of Computational Chemistry. 9: 327-335. DOI: 10.1002/Jcc.540090407  0.549
1987 Gilson MK, Honig BH. Calculation of electrostatic potentials in an enzyme active site. Nature. 330: 84-6. PMID 3313058 DOI: 10.1038/330084A0  0.57
1986 Gilson MK, Honig BH. The dielectric constant of a folded protein. Biopolymers. 25: 2097-119. PMID 3790703 DOI: 10.1002/Bip.360251106  0.516
1985 Gilson MK, Rashin A, Fine R, Honig B. On the calculation of electrostatic interactions in proteins Journal of Molecular Biology. 184: 503-516. PMID 4046024 DOI: 10.1016/0022-2836(85)90297-9  0.57
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