Michael Gilson | UCSD Profiles

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Assessment of Pharmaceutical Protein-Ligand Pose and Affinity Predictions in CASP16. Proteins. 2026 Jan; 94(1):249-266. Gilson MK, Eberhardt J, Škrinjar P, Durairaj J, Robin X, Kryshtafovych A. PMID: 41045049; PMCID: PMC12750038.

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HumansCells

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Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v1.0]. Living J Comput Mol Sci. 2025 Jul 12; 6(1). Cavender CE, Case DA, Chen JC, Chong LT, Keedy DA, Lindorff-Larsen K, Mobley DL, Ollila OHS, Oostenbrink C, Robustelli P, Voelz VA, Wall ME, Wych DC, Gilson MK. PMID: 41573260; PMCID: PMC12823150.

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A Simple, Polarizable, Rigid, 3-Point Water Model Using the Direct Polarization Approximation. J Chem Theory Comput. 2025 Jul 22; 21(14):6964-6978. Drew LW, Gilson MK. PMID: 40621891; PMCID: PMC12476135.

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Thermodynamics of Water Displacement from Binding Sites and its Contributions to Supramolecular and Biomolecular Affinity. Angew Chem Int Ed Engl. 2025 Aug 25; 64(35):e202505713. Setiadi J, Biedermann F, Nau WM, Gilson MK. PMID: 40468161; PMCID: PMC12377430.

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Computation of Protein-Ligand Binding Free Energies with a Quantum Mechanics-Based Mining Minima Algorithm. J Chem Theory Comput. 2025 Apr 22; 21(8):4236-4265. Schlinsog M, Sattasathuchana T, Xu P, Guidez EB, Gilson MK, Potter MJ, Gordon MS, Webb SP. PMID: 40202178; PMCID: PMC12020368.

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Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v0.1]. ArXiv. 2025 Mar 25. Cavender CE, Case DA, Chen JC, Chong LT, Keedy DA, Lindorff-Larsen K, Mobley DL, Ollila OHS, Oostenbrink C, Robustelli P, Voelz VA, Wall ME, Wych DC, Gilson MK. PMID: 40196146; PMCID: PMC11975311.

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Revisiting the Plasmodium falciparum druggable genome using predicted structures and data mining. NPJ Drug Discov. 2025; 2(1):3. Godinez-Macias KP, Chen D, Wallis JL, Siegel MG, Adam A, Bopp S, Carolino K, Coulson LB, Durst G, Thathy V, Esherick L, Farringer MA, Flannery EL, Forte B, Liu T, Godoy Magalhaes L, Gupta AK, Istvan ES, Jiang T, Kumpornsin K, Lobb K, McLean KJ, Moura IMR, Okombo J, Payne NC, Plater A, Rao SPS, Siqueira-Neto JL, Somsen BA, Summers RL, Zhang R, Gilson MK, Gamo FJ, Campo B, Baragaña B, Duffy J, Gilbert IH, Lukens AK, Dechering KJ, Niles JC, McNamara CW, Cheng X, Birkholtz LM, Bronkhorst AW, Fidock DA, Wirth DF, Goldberg DE, Lee MCS, Winzeler EA. PMID: 40066064; PMCID: PMC11892419.

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The Need for Continuing Blinded Pose- and Activity Prediction Benchmarks. J Chem Inf Model. 2025 Mar 10; 65(5):2180-2190. Kramer C, Chodera J, Damm-Ganamet KL, Gilson MK, Günther J, Lessel U, Lewis RA, Mobley D, Nittinger E, Pecina A, Schapira M, Walters WP. PMID: 39951479; PMCID: PMC12818095.

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BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data. Nucleic Acids Res. 2025 Jan 06; 53(D1):D1633-D1644. Liu T, Hwang L, Burley SK, Nitsche CI, Southan C, Walters WP, Gilson MK. PMID: 39574417; PMCID: PMC11701568.

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Revisiting the Plasmodium falciparum druggable genome using predicted structures and data mining. Res Sq. 2024 Nov 26. Godinez-Macias KP, Chen D, Wallis JL, Siegel MG, Adam A, Bopp S, Carolino K, Coulson LB, Durst G, Thathy V, Esherick L, Farringer MA, Flannery EL, Forte B, Liu T, Magalhaes LG, Gupta AK, Istvan ES, Jiang T, Kumpornsin K, Lobb K, McLean K, Moura IMR, Okombo J, Payne NC, Plater A, Rao SPS, Siqueira-Neto JL, Somsen BA, Summers RL, Zhang R, Gilson MK, Gamo FJ, Campo B, Baragaña B, Duffy J, Gilbert IH, Lukens AK, Dechering KJ, Niles JC, McNamara CW, Cheng X, Birkholtz LM, Bronkhorst AW, Fidock DA, Wirth DF, Goldberg DE, Lee MCS, Winzeler EA. PMID: 39649165; PMCID: PMC11623766.

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Correction to "BAT2: an Open-Source Tool for Flexible, Automated, and Low Cost Absolute Binding Free Energy Calculations". J Chem Theory Comput. 2024 Oct 08; 20(19):8740. Heinzelmann G, Huggins DJ, Gilson MK. PMID: 39286862; PMCID: PMC11465461.

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BAT2: an Open-Source Tool for Flexible, Automated, and Low Cost Absolute Binding Free Energy Calculations. J Chem Theory Comput. 2024 Aug 13; 20(15):6518-6530. Heinzelmann G, Huggins DJ, Gilson MK. PMID: 39088306; PMCID: PMC11325538.

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The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling. J Phys Chem B. 2024 Jul 25; 128(29):7043-7067. Wang L, Behara PK, Thompson MW, Gokey T, Wang Y, Wagner JR, Cole DJ, Gilson MK, Shirts MR, Mobley DL. PMID: 38989715; PMCID: PMC11284797.

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Rapid, Accurate, Ranking of Protein-Ligand Binding Affinities with VM2, the Second-Generation Mining Minima Method. J Chem Theory Comput. 2024 Jul 23; 20(14):6328-6340. Gilson MK, Stewart LE, Potter MJ, Webb SP. PMID: 38989926; PMCID: PMC11392596.

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Ligand-Based Compound Activity Prediction via Few-Shot Learning. J Chem Inf Model. 2024 Jul 22; 64(14):5492-5499. Eckmann P, Anderson J, Yu R, Gilson MK. PMID: 38950281; PMCID: PMC11267577.

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Free Energy Density of a Fluid and Its Role in Solvation and Binding. J Chem Theory Comput. 2024 Apr 09; 20(7):2871-2887. Gilson MK, Kurtzman T. PMID: 38536144; PMCID: PMC11197885.

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A Fast, Convenient, Polarizable Electrostatic Model for Molecular Dynamics. J Chem Theory Comput. 2024 Feb 13; 20(3):1293-1305. Wang L, Schauperl M, Mobley DL, Bayly C, Gilson MK. PMID: 38240687; PMCID: PMC10867846.

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Host-guest systems for the SAMPL9 blinded prediction challenge: phenothiazine as a privileged scaffold for binding to cyclodextrins. Phys Chem Chem Phys. 2024 Jan 17; 26(3):2035-2043. Andrade B, Chen A, Gilson MK. PMID: 38126539; PMCID: PMC10832227.

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Tuning Potential Functions to Host-Guest Binding Data. J Chem Theory Comput. 2024 Jan 09; 20(1):239-252. Setiadi J, Boothroyd S, Slochower DR, Dotson DL, Thompson MW, Wagner JR, Wang LP, Gilson MK. PMID: 38147689; PMCID: PMC10838530.

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Target-Free Compound Activity Prediction via Few-Shot Learning. ArXiv. 2023 Nov 27. Eckmann P, Anderson J, Gilson MK, Yu R. PMID: 38076516; PMCID: PMC10705577.

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The temperature-dependence of host-guest binding thermodynamics: experimental and simulation studies. Chem Sci. 2023 Nov 01; 14(42):11818-11829. Grimm LM, Setiadi J, Tkachenko B, Schreiner PR, Gilson MK, Biedermann F. PMID: 37920355; PMCID: PMC10619620.

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Structure-Activity Relationships, Tolerability and Efficacy of Microtubule-Active 1,2,4-Triazolo[1,5-a]pyrimidines as Potential Candidates to Treat Human African Trypanosomiasis. ChemMedChem. 2023 10 17; 18(20):e202300193. Monti L, Liu LJ, Varricchio C, Lucero B, Alle T, Yang W, Bem-Shalom I, Gilson M, Brunden KR, Brancale A, Caffrey CR, Ballatore C. PMID: 37429821; PMCID: PMC10615688.

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Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field. J Chem Theory Comput. 2023 Jun 13; 19(11):3251-3275. Boothroyd S, Behara PK, Madin OC, Hahn DF, Jang H, Gapsys V, Wagner JR, Horton JT, Dotson DL, Thompson MW, Maat J, Gokey T, Wang LP, Cole DJ, Gilson MK, Chodera JD, Bayly CI, Shirts MR, Mobley DL. PMID: 37167319; PMCID: PMC10269353.

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Structure-Activity Relationships, Tolerability and Efficacy of Microtubule-Active 1,2,4-Triazolo[1,5- a ]pyrimidines as Potential Candidates to Treat Human African Trypanosomiasis. bioRxiv. 2023 Mar 11. Monti L, Liu LJ, Varricchio C, Lucero B, Alle T, Yang W, Bem-Shalom I, Gilson M, Brunden KR, Brancale A, Caffrey CR, Ballatore C. PMID: 36945407; PMCID: PMC10028969.

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Development of Potent and Highly Selective Epoxyketone-Based Plasmodium Proteasome Inhibitors. Chemistry. 2023 Apr 06; 29(20):e202203958. Almaliti J, Fajtová P, Calla J, LaMonte GM, Feng M, Rocamora F, Ottilie S, Glukhov E, Boura E, Suhandynata RT, Momper JD, Gilson MK, Winzeler EA, Gerwick WH, O'Donoghue AJ. PMID: 36617500; PMCID: PMC10894724.

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Absolute binding free energy calculations improve enrichment of actives in virtual compound screening. Sci Rep. 2022 08 10; 12(1):13640. Feng M, Heinzelmann G, Gilson MK. PMID: 35948614; PMCID: PMC9365818.

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LIMO: Latent Inceptionism for Targeted Molecule Generation. Proc Mach Learn Res. 2022 Jul; 162:5777-5792. Eckmann P, Sun K, Zhao B, Feng M, Gilson MK, Yu R. PMID: 36193121; PMCID: PMC9527083.

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Building a Precision Medicine Delivery Platform for Clinics: The University of California, San Francisco, BRIDGE Experience. J Med Internet Res. 2022 02 15; 24(2):e34560. Bove R, Schleimer E, Sukhanov P, Gilson M, Law SM, Barnecut A, Miller BL, Hauser SL, Sanders SJ, Rankin KP. PMID: 35166689; PMCID: PMC8889486.

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CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-finding. Nat Rev Chem. 2022 Apr; 6(4):287-295. Ackloo S, Al-Awar R, Amaro RE, Arrowsmith CH, Azevedo H, Batey RA, Bengio Y, Betz UAK, Bologa CG, Chodera JD, Cornell WD, Dunham I, Ecker GF, Edfeldt K, Edwards AM, Gilson MK, Gordijo CR, Hessler G, Hillisch A, Hogner A, Irwin JJ, Jansen JM, Kuhn D, Leach AR, Lee AA, Lessel U, Morgan MR, Moult J, Muegge I, Oprea TI, Perry BG, Riley P, Rousseaux SAL, Saikatendu KS, Santhakumar V, Schapira M, Scholten C, Todd MH, Vedadi M, Volkamer A, Willson TM. PMID: 35783295; PMCID: PMC9246350.

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Stimuli Induced Uptake of Protein-Like Peptide Brush Polymers. Chemistry. 2022 Jan 24; 28(5):e202103438. Blum AP, Yin J, Lin HH, Oliver BA, Kammeyer JK, Thompson MP, Gilson MK, Gianneschi NC. PMID: 34811828; PMCID: PMC8861929.

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Fast Equilibration of Water between Buried Sites and the Bulk by Molecular Dynamics with Parallel Monte Carlo Water Moves on Graphical Processing Units. J Chem Theory Comput. 2021 Dec 14; 17(12):7366-7372. Ben-Shalom IY, Lin C, Radak BK, Sherman W, Gilson MK. PMID: 34762421; PMCID: PMC8716912.

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Improving Structure-Based Virtual Screening with Ensemble Docking and Machine Learning. J Chem Inf Model. 2021 11 22; 61(11):5362-5376. Ricci-Lopez J, Aguila SA, Gilson MK, Brizuela CA. PMID: 34652141; PMCID: PMC8865842.

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Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field. J Chem Theory Comput. 2021 Oct 12; 17(10):6262-6280. Qiu Y, Smith DGA, Boothroyd S, Jang H, Hahn DF, Wagner J, Bannan CC, Gokey T, Lim VT, Stern CD, Rizzi A, Tjanaka B, Tresadern G, Lucas X, Shirts MR, Gilson MK, Chodera JD, Bayly CI, Mobley DL, Wang LP. PMID: 34551262; PMCID: PMC8511297.

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Mechanistic analysis of light-driven overcrowded alkene-based molecular motors by multiscale molecular simulations. Phys Chem Chem Phys. 2021 Apr 14; 23(14):8525-8540. Feng M, Gilson MK. PMID: 33876015; PMCID: PMC8102045.

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Automation of absolute protein-ligand binding free energy calculations for docking refinement and compound evaluation. Sci Rep. 2021 01 13; 11(1):1116. Heinzelmann G, Gilson MK. PMID: 33441879; PMCID: PMC7806944.

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Whole-Brain Image Analysis and Anatomical Atlas 3D Generation Using MagellanMapper. Curr Protoc Neurosci. 2020 12; 94(1):e104. Young DM, Duhn C, Gilson M, Nojima M, Yuruk D, Kumar A, Yu W, Sanders SJ. PMID: 32981139; PMCID: PMC7781073.

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Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations. J Chem Theory Comput. 2020 Dec 08; 16(12):7883-7894. Ben-Shalom IY, Lin Z, Radak BK, Lin C, Sherman W, Gilson MK. PMID: 33206520; PMCID: PMC7725968.

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Data-driven analysis of the number of Lennard-Jones types needed in a force field. Commun Chem. 2020; 3(1). Schauperl M, Kantonen S, Wang LP, Gilson MK. PMID: 34295996; PMCID: PMC8294475.

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Experimental characterization of the association of β-cyclodextrin and eight novel cyclodextrin derivatives with two guest compounds. J Comput Aided Mol Des. 2021 01; 35(1):95-104. Kellett K, Slochower DR, Schauperl M, Duggan BM, Gilson MK. PMID: 33037548; PMCID: PMC7867601.

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Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo. J Comput Aided Mol Des. 2021 02; 35(2):167-177. Bergazin TD, Ben-Shalom IY, Lim NM, Gill SC, Gilson MK, Mobley DL. PMID: 32968887; PMCID: PMC7904576.

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Non-bonded force field model with advanced restrained electrostatic potential charges (RESP2). Commun Chem. 2020; 3. Schauperl M, Nerenberg PS, Jang H, Wang LP, Bayly CI, Mobley DL, Gilson MK. PMID: 34136662; PMCID: PMC8204736.

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Drug Design Data Resource, Grand Challenge 4, second of two issues. J Comput Aided Mol Des. 2020 02; 34(2):97. Gilson MK, Amaro RE. PMID: 32016636.

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The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. J Comput Aided Mol Des. 2020 05; 34(5):601-633. 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, Mobley DL, Chodera JD. PMID: 31984465; PMCID: PMC7282318.

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D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. J Comput Aided Mol Des. 2020 02; 34(2):99-119. 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. PMID: 31974851; PMCID: PMC7261493.

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Data-Driven Mapping of Gas-Phase Quantum Calculations to General Force Field Lennard-Jones Parameters. J Chem Theory Comput. 2020 Feb 11; 16(2):1115-1127. Kantonen SM, Muddana HS, Schauperl M, Henriksen NM, Wang LP, Gilson MK. PMID: 31917572; PMCID: PMC7101068.

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Binding Thermodynamics of Host-Guest Systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative. J Chem Theory Comput. 2019 Nov 12; 15(11):6225-6242. Slochower DR, Henriksen NM, Wang LP, Chodera JD, Mobley DL, Gilson MK. PMID: 31603667; PMCID: PMC7328435.

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Antitumor Activity of 1,18-Octadecanedioic Acid-Paclitaxel Complexed with Human Serum Albumin. J Am Chem Soc. 2019 07 31; 141(30):11765-11769. 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, Gianneschi NC. PMID: 31317744; PMCID: PMC6676409.

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A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site. PLoS One. 2019; 14(7):e0219473. Nguyen C, Yamazaki T, Kovalenko A, Case DA, Gilson MK, Kurtzman T, Luchko T. PMID: 31291328; PMCID: PMC6619770.

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Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking. Structure. 2019 08 06; 27(8):1326-1335.e4. Wagner JR, Churas CP, Liu S, Swift RV, Chiu M, Shao C, Feher VA, Burley SK, Gilson MK, Amaro RE. PMID: 31257108; PMCID: PMC6685748.

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Entropic effects enable life at extreme temperatures. Sci Adv. 2019 05; 5(5):eaaw4783. Kim YH, Leriche G, Diraviyam K, Koyanagi T, Gao K, Onofrei D, Patterson J, Guha A, Gianneschi N, Holland GP, Gilson MK, Mayer M, Sept D, Yang J. PMID: 31049402; PMCID: PMC6494508.

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A Thermodynamic Limit on the Role of Self-Propulsion in Enhanced Enzyme Diffusion. Biophys J. 2019 05 21; 116(10):1898-1906. Feng M, Gilson MK. PMID: 31053258; PMCID: PMC6531786.

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Simulating Water Exchange to Buried Binding Sites. J Chem Theory Comput. 2019 Apr 09; 15(4):2684-2691. Ben-Shalom IY, Lin C, Kurtzman T, Walker RC, Gilson MK. PMID: 30835999; PMCID: PMC6456390.

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D3R Grand Challenge 3: blind prediction of protein-ligand poses and affinity rankings. J Comput Aided Mol Des. 2019 01; 33(1):1-18. 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. PMID: 30632055; PMCID: PMC6472484.

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Toward Learned Chemical Perception of Force Field Typing Rules. J Chem Theory Comput. 2019 Jan 08; 15(1):402-423. Zanette C, Bannan CC, Bayly CI, Fass J, Gilson MK, Shirts MR, Chodera JD, Mobley DL. PMID: 30512951; PMCID: PMC6467725.

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Discovering de novo peptide substrates for enzymes using machine learning. Nat Commun. 2018 12 07; 9(1):5253. Tallorin L, Wang J, Kim WE, Sahu S, Kosa NM, Yang P, Thompson M, Gilson MK, Frazier PI, Burkart MD, Gianneschi NC. PMID: 30531862; PMCID: PMC6286390.

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Overview of the SAMPL6 host-guest binding affinity prediction challenge. J Comput Aided Mol Des. 2018 10; 32(10):937-963. Rizzi A, Murkli S, McNeill JN, Yao W, Sullivan M, Gilson MK, Chiu MW, Isaacs L, Gibb BC, Mobley DL, Chodera JD. PMID: 30415285; PMCID: PMC6301044.

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Escaping Atom Types in Force Fields Using Direct Chemical Perception. J Chem Theory Comput. 2018 Nov 13; 14(11):6076-6092. Mobley DL, Bannan CC, Rizzi A, Bayly CI, Chodera JD, Lim VT, Lim NM, Beauchamp KA, Slochower DR, Shirts MR, Gilson MK, Eastman PK. PMID: 30351006; PMCID: PMC6245550.

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Protein-ligand binding enthalpies from near-millisecond simulations: Analysis of a preorganization paradox. J Chem Phys. 2018 Aug 21; 149(7):072311. Li A, Gilson MK. PMID: 30134726; PMCID: PMC5962444.

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Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate. Nat Commun. 2018 08 06; 9(1):3085. Chen SF, Huang NL, Lin JH, Wu CC, Wang YR, Yu YJ, Gilson MK, Chan NL. PMID: 30082834; PMCID: PMC6078968.

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Bind3P: Optimization of a Water Model Based on Host-Guest Binding Data. J Chem Theory Comput. 2018 Jul 10; 14(7):3621-3632. Yin J, Henriksen NM, Muddana HS, Gilson MK. PMID: 29874074; PMCID: PMC6039243.

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16  

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Motor-like Properties of Nonmotor Enzymes. Biophys J. 2018 05 08; 114(9):2174-2179. Slochower DR, Gilson MK. PMID: 29742410; PMCID: PMC5961456.

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   Mentions:

8  

   Fields: 

   Translation:

Cells

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PubMed

   Mentions:

6  

   Fields: 

   

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PubMed

   Mentions:

42  

   Fields: 

   Translation:

Cells

Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories. J Chem Theory Comput. 2018 Jan 09; 14(1):418-425. Haider K, Cruz A, Ramsey S, Gilson MK, Kurtzman T. PMID: 29161510; PMCID: PMC5760325.

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PubMed

   Mentions:

20  

   Fields: 

   

Accounting for apparent deviations between calorimetric and van't Hoff enthalpies. Biochim Biophys Acta Gen Subj. 2018 Mar; 1862(3):692-704. Kantonen SA, Henriksen NM, Gilson MK. PMID: 29221984; PMCID: PMC5851798.

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PubMed

   Mentions:

4  

   Fields: 

   Translation:

Cells

D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. J Comput Aided Mol Des. 2018 01; 32(1):1-20. 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. PMID: 29204945; PMCID: PMC5767524.

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PubMed

   Mentions:

94  

   Fields: 

   Translation:

HumansCells

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. J Phys Chem B. 2017 12 14; 121(49):11144-11162. Assaf KI, Florea M, Antony J, Henriksen NM, Yin J, Hansen A, Qu ZW, Sure R, Klapstein D, Gilson MK, Grimme S, Nau WM. PMID: 29140701; PMCID: PMC6247792.

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PubMed

   Mentions:

19  

   Fields: 

   Translation:

Cells

Nonparametric test for connectivity detection in multivariate autoregressive networks and application to multiunit activity data. Netw Neurosci. 2018; 1(4):357-380. Gilson M, Tauste Campo A, Chen X, Thiele A, Deco G. PMID: 30090871; PMCID: PMC6063719.

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PubMed

   Mentions:

8  

Evaluating Force Field Performance in Thermodynamic Calculations of Cyclodextrin Host-Guest Binding: Water Models, Partial Charges, and Host Force Field Parameters. J Chem Theory Comput. 2017 Sep 12; 13(9):4253-4269. Henriksen NM, Gilson MK. PMID: 28696692; PMCID: PMC5606194.

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PubMed

   Mentions:

19  

   Fields: 

   

Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. J Comput Aided Mol Des. 2017 08; 31(8):777. Shirts MR, Klein C, Swails JM, Yin J, Gilson MK, Mobley DL, Case DA, Zhong ED. PMID: 28752343.

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PubMed

   Mentions:

3  

   Fields: 

   

Testing inhomogeneous solvation theory in structure-based ligand discovery. Proc Natl Acad Sci U S A. 2017 08 15; 114(33):E6839-E6846. Balius TE, Fischer M, Stein RM, Adler TB, Nguyen CN, Cruz A, Gilson MK, Kurtzman T, Shoichet BK. PMID: 28760952; PMCID: PMC5565424.

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PubMed

   Mentions:

38  

   Fields: 

   Translation:

Cells

Attach-Pull-Release Calculations of Ligand Binding and Conformational Changes on the First BRD4 Bromodomain. J Chem Theory Comput. 2017 Jul 11; 13(7):3260-3275. Heinzelmann G, Henriksen NM, Gilson MK. PMID: 28564537; PMCID: PMC5541932.

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PubMed

   Mentions:

28  

   Fields: 

   Translation:

HumansCells

Attractive Interactions between Heteroallenes and the Cucurbituril Portal. J Am Chem Soc. 2017 06 21; 139(24):8138-8145. Reany O, Li A, Yefet M, Gilson MK, Keinan E. PMID: 28532152; PMCID: PMC5581494.

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PubMed

   Mentions:

4  

   Fields: 

   

Bio-inspired CO2 reduction by a rhenium tricarbonyl bipyridine-based catalyst appended to amino acids and peptidic platforms: incorporating proton relays and hydrogen-bonding functional groups. Faraday Discuss. 2017 06 02; 198:279-300. Chabolla SA, Machan CW, Yin J, Dellamary EA, Sahu S, Gianneschi NC, Gilson MK, Tezcan FA, Kubiak CP. PMID: 28374024; PMCID: PMC5604230.

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PubMed

   Mentions:

7  

   Fields: 

   Translation:

Cells

Predicting Binding Free Energies: Frontiers and Benchmarks. Annu Rev Biophys. 2017 05 22; 46:531-558. Mobley DL, Gilson MK. PMID: 28399632; PMCID: PMC5544526.

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   Mentions:

148  

   Fields: 

   Translation:

Cells

Probing the orientation of inhibitor and epoxy-eicosatrienoic acid binding in the active site of soluble epoxide hydrolase. Arch Biochem Biophys. 2017 Jan 01; 613:1-11. Lee KS, Henriksen NM, Ng CJ, Yang J, Jia W, Morisseau C, Andaya A, Gilson MK, Hammock BD. PMID: 27983948; PMCID: PMC5172606.

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PubMed

   Mentions:

6  

   Fields: 

   Translation:

HumansCells

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. J Comput Aided Mol Des. 2017 01; 31(1):147-161. Shirts MR, Klein C, Swails JM, Yin J, Gilson MK, Mobley DL, Case DA, Zhong ED. PMID: 27787702; PMCID: PMC5581938.

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PubMed

   Mentions:

129  

   Fields: 

   Translation:

Cells

D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions. J Comput Aided Mol Des. 2016 09; 30(9):651-668. 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. PMID: 27696240; PMCID: PMC5562487.

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PubMed

   Mentions:

115  

   Fields: 

   Translation:

Cells

Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge. J Comput Aided Mol Des. 2016 11; 30(11):927-944. Bannan CC, Burley KH, Chiu M, Shirts MR, Gilson MK, Mobley DL. PMID: 27677750; PMCID: PMC5209301.

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PubMed

   Mentions:

62  

   Fields: 

   Translation:

Cells

Overview of the SAMPL5 host-guest challenge: Are we doing better? J Comput Aided Mol Des. 2017 01; 31(1):1-19. Yin J, Henriksen NM, Slochower DR, Shirts MR, Chiu MW, Mobley DL, Gilson MK. PMID: 27658802; PMCID: PMC5241188.

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PubMed

   Mentions:

86  

   Fields: 

   Translation:

Cells

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. 2017 01; 31(1):133-145. Yin J, Henriksen NM, Slochower DR, Gilson MK. PMID: 27638809; PMCID: PMC5241238.

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PubMed

   Mentions:

24  

   Fields: 

   Translation:

Cells

Evaluation and Minimization of Uncertainty in ITC Binding Measurements: Heat Error, Concentration Error, Saturation, and Stoichiometry. Biochim Biophys Acta Gen Subj. 2017 Feb; 1861(2):485-498. Kantonen SA, Henriksen NM, Gilson MK. PMID: 27599357; PMCID: PMC5195854.

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PubMed

   Mentions:

14  

   Fields: 

   Translation:

Cells

Erratum: "The electrostatic response of water to neutral polar solutes: Implications for continuum solvent modeling" [J. Chem. Phys. 138, 224504 (2013)]. J Chem Phys. 2016 07 28; 145(4):049902. Muddana HS, Sapra NV, Fenley AT, Gilson MK. PMID: 27475401; PMCID: PMC6910594.

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   Fields: 

   

Improving the Efficiency and Activity of Electrocatalysts for the Reduction of CO2 through Supramolecular Assembly with Amino Acid-Modified Ligands. J Am Chem Soc. 2016 07 06; 138(26):8184-93. Machan CW, Yin J, Chabolla SA, Gilson MK, Kubiak CP. PMID: 27258781.

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PubMed

   Mentions:

9  

   Fields: 

   Translation:

Cells

Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST. J Comput Chem. 2016 08 05; 37(21):2029-37. Ramsey S, Nguyen C, Salomon-Ferrer R, Walker RC, Gilson MK, Kurtzman T. PMID: 27317094; PMCID: PMC5052087.

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PubMed

   Mentions:

56  

   Fields: 

   Translation:

Cells

Evaluation of Representations and Response Models for Polarizable Force Fields. J Phys Chem B. 2016 08 25; 120(33):8668-84. Li A, Voronin A, Fenley AT, Gilson MK. PMID: 27248842; PMCID: PMC5002935.

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PubMed

   Mentions:

2  

   Fields: 

   

Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces. J Phys Chem B. 2016 09 01; 120(34):8743-56. Haider K, Wickstrom L, Ramsey S, Gilson MK, Kurtzman T. PMID: 27169482; PMCID: PMC5009012.

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   Mentions:

15  

   Fields: 

   Translation:

Cells

Spatial Decomposition of Translational Water-Water Correlation Entropy in Binding Pockets. J Chem Theory Comput. 2016 Jan 12; 12(1):414-29. Nguyen CN, Kurtzman T, Gilson MK. PMID: 26636620; PMCID: PMC4819442.

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PubMed

   Mentions:

18  

   Fields: 

   Translation:

Cells

BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology. Nucleic Acids Res. 2016 Jan 04; 44(D1):D1045-53. Gilson MK, Liu T, Baitaluk M, Nicola G, Hwang L, Chong J. PMID: 26481362; PMCID: PMC4702793.

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PubMed

   Mentions:

619  

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Cells

Binding enthalpy calculations for a neutral host-guest pair yield widely divergent salt effects across water models. J Chem Theory Comput. 2015 Oct 13; 11(10):4555-64. Gao K, Yin J, Henriksen NM, Fenley AT, Gilson MK. PMID: 26574247; PMCID: PMC4668924.

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PubMed

   Mentions:

23  

   Fields: 

   Translation:

Cells

Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME. Database (Oxford). 2015; 2015. Nicola G, Berthold MR, Hedrick MP, Gilson MK. PMID: 26384374; PMCID: PMC4572361.

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   Mentions:

11  

   Fields: 

   Translation:

HumansAnimalsCells

Computational Calorimetry: High-Precision Calculation of Host-Guest Binding Thermodynamics. J Chem Theory Comput. 2015 Sep 08; 11(9):4377-94. Henriksen NM, Fenley AT, Gilson MK. PMID: 26523125; PMCID: PMC4614838.

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   Mentions:

52  

   Fields: 

   Translation:

Cells

Parameterization of an effective potential for protein-ligand binding from host-guest affinity data. J Mol Recognit. 2016 Jan; 29(1):10-21. Wickstrom L, Deng N, He P, Mentes A, Nguyen C, Gilson MK, Kurtzman T, Gallicchio E, Levy RM. PMID: 26256816; PMCID: PMC4715590.

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PubMed

   Mentions:

21  

   Fields: 

   Translation:

Cells

Toward Improved Force-Field Accuracy through Sensitivity Analysis of Host-Guest Binding Thermodynamics. J Phys Chem B. 2015 Aug 13; 119(32):10145-55. Yin J, Fenley AT, Henriksen NM, Gilson MK. PMID: 26181208; PMCID: PMC4664157.

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   Mentions:

19  

   Fields: 

   Translation:

Cells

Calculation and visualization of atomistic mechanical stresses in nanomaterials and biomolecules. PLoS One. 2014; 9(12):e113119. Fenley AT, Muddana HS, Gilson MK. PMID: 25503996; PMCID: PMC4263534.

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   Mentions:

2  

   Fields: 

   Translation:

AnimalsCells

Dynamic architecture of a protein kinase. Proc Natl Acad Sci U S A. 2014 Oct 28; 111(43):E4623-31. McClendon CL, Kornev AP, Gilson MK, Taylor SS. PMID: 25319261; PMCID: PMC4217441.

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   Mentions:

137  

   Fields: 

   Translation:

Cells

Peptides displayed as high density brush polymers resist proteolysis and retain bioactivity. J Am Chem Soc. 2014 Oct 29; 136(43):15422-37. Blum AP, Kammeyer JK, Yin J, Crystal DT, Rush AM, Gilson MK, Gianneschi NC. PMID: 25314576; PMCID: PMC4227725.

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PubMed

   Mentions:

31  

   Fields: 

   Translation:

HumansCells

Supramolecular assembly promotes the electrocatalytic reduction of carbon dioxide by Re(I) bipyridine catalysts at a lower overpotential. J Am Chem Soc. 2014 Oct 15; 136(41):14598-607. Machan CW, Chabolla SA, Yin J, Gilson MK, Tezcan FA, Kubiak CP. PMID: 25226161.

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   Mentions:

22  

   Fields: 

   Translation:

Cells

Bridging Calorimetry and Simulation through Precise Calculations of Cucurbituril-Guest Binding Enthalpies. J Chem Theory Comput. 2014 Sep 09; 10(9):4069-4078. Fenley AT, Henriksen NM, Muddana HS, Gilson MK. PMID: 25221445; PMCID: PMC4159218.

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PubMed

   Mentions:

42  

   Fields: 

   

Correlation as a determinant of configurational entropy in supramolecular and protein systems. J Phys Chem B. 2014 Jun 19; 118(24):6447-55. Fenley AT, Killian BJ, Hnizdo V, Fedorowicz A, Sharp DS, Gilson MK. PMID: 24702693; PMCID: PMC4067153.

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   Mentions:

11  

   Fields: 

   Translation:

AnimalsCells

Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa. J Chem Theory Comput. 2014 Jul 08; 10(7):2769-2780. Nguyen CN, Cruz A, Gilson MK, Kurtzman T. PMID: 25018673; PMCID: PMC4089914.

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   Mentions:

68  

   Fields: 

   

The SAMPL4 host-guest blind prediction challenge: an overview. J Comput Aided Mol Des. 2014 Apr; 28(4):305-17. Muddana HS, Fenley AT, Mobley DL, Gilson MK. PMID: 24599514; PMCID: PMC4053502.

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   Mentions:

102  

   Fields: 

   Translation:

Cells

Quantum Mechanical Calculation of Noncovalent Interactions: A Large-Scale Evaluation of PMx, DFT, and SAPT Approaches. J Chem Theory Comput. 2014 Apr 08; 10(4):1563-1575. Li A, Muddana HS, Gilson MK. PMID: 24803867; PMCID: PMC3985464.

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   Mentions:

20  

   Fields: 

   

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PubMed

   Mentions:

8  

   Fields: 

   

Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method. J Comput Aided Mol Des. 2014 Apr; 28(4):463-74. Muddana HS, Yin J, Sapra NV, Fenley AT, Gilson MK. PMID: 24510191; PMCID: PMC4053532.

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   Mentions:

10  

   Fields: 

   Translation:

Cells

The SAMPL4 hydration challenge: evaluation of partial charge sets with explicit-water molecular dynamics simulations. J Comput Aided Mol Des. 2014 Mar; 28(3):277-87. Muddana HS, Sapra NV, Fenley AT, Gilson MK. PMID: 24477800; PMCID: PMC4006311.

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   Mentions:

17  

   Fields: 

   Translation:

Cells

Overcoming dissipation in the calculation of standard binding free energies by ligand extraction. J Comput Chem. 2013 Oct 15; 34(27):2360-71. Velez-Vega C, Gilson MK. PMID: 24038118; PMCID: PMC3932244.

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PubMed

   Mentions:

37  

   Fields: 

   Translation:

Cells

Inhibitory synaptic plasticity: spike timing-dependence and putative network function. Front Neural Circuits. 2013; 7:119. Vogels TP, Froemke RC, Doyon N, Gilson M, Haas JS, Liu R, Maffei A, Miller P, Wierenga CJ, Woodin MA, Zenke F, Sprekeler H. PMID: 23882186; PMCID: PMC3714539.

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   Mentions:

65  

   Fields: 

   Translation:

HumansAnimalsCells

The electrostatic response of water to neutral polar solutes: implications for continuum solvent modeling. J Chem Phys. 2013 Jun 14; 138(22):224504. Muddana HS, Sapra NV, Fenley AT, Gilson MK. PMID: 23781802; PMCID: PMC3695974.

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PubMed

   Mentions:

9  

   Fields: 

   

Entropy-enthalpy transduction caused by conformational shifts can obscure the forces driving protein-ligand binding. Proc Natl Acad Sci U S A. 2012 Dec 04; 109(49):20006-11. Fenley AT, Muddana HS, Gilson MK. PMID: 23150595; PMCID: PMC3523842.

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PubMed

   Mentions:

51  

   Fields: 

   Translation:

AnimalsCells

Ten years of standardizing proteomic data: a report on the HUPO-PSI Spring Workshop: April 12-14th, 2012, San Diego, USA. Proteomics. 2012 Sep; 12(18):2767-72. Orchard S, Binz PA, Borchers C, Gilson MK, Jones AR, Nicola G, Vizcaino JA, Deutsch EW, Hermjakob H. PMID: 22969026; PMCID: PMC3895333.

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PubMed

   Mentions:

8  

   Fields: 

   Translation:

Humans

Grid inhomogeneous solvation theory: hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril. J Chem Phys. 2012 Jul 28; 137(4):044101. Nguyen CN, Young TK, Gilson MK. PMID: 22852591; PMCID: PMC3416872.

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   Mentions:

155  

   Fields: 

   Translation:

Cells

Public domain databases for medicinal chemistry. J Med Chem. 2012 Aug 23; 55(16):6987-7002. Nicola G, Liu T, Gilson MK. PMID: 22731701; PMCID: PMC3427776.

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   Mentions:

20  

   Fields: 

   

Charge Optimization Theory for Induced-Fit Ligands. J Chem Theory Comput. 2012 Nov 13; 8(11):4580-4592. Shen Y, Gilson MK, Tidor B. PMID: 23162383; PMCID: PMC3496346.

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   Mentions:

2  

   Fields: 

   

The Fundamental Role of Flexibility on the Strength of Molecular Binding. Soft Matter. 2012; 8(23):6385-6392. Forrey C, Douglas JF, Gilson MK. PMID: 22707976; PMCID: PMC3374587.

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   Mentions:

24  

   Fields: 

   

Calculation of Host-Guest Binding Affinities Using a Quantum-Mechanical Energy Model. J Chem Theory Comput. 2012 Jun 12; 8(6):2023-2033. Muddana HS, Gilson MK. PMID: 22737045; PMCID: PMC3378313.

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PubMed

   Mentions:

23  

   Fields: 

   

The carmaphycins: new proteasome inhibitors exhibiting an α,β-epoxyketone warhead from a marine cyanobacterium. Chembiochem. 2012 Apr 16; 13(6):810-7. Pereira AR, Kale AJ, Fenley AT, Byrum T, Debonsi HM, Gilson MK, Valeriote FA, Moore BS, Gerwick WH. PMID: 22383253; PMCID: PMC3393770.

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PubMed

   Mentions:

60  

   Fields: 

   Translation:

AnimalsCells

Blind prediction of host-guest binding affinities: a new SAMPL3 challenge. J Comput Aided Mol Des. 2012 May; 26(5):475-87. Muddana HS, Varnado CD, Bielawski CW, Urbach AR, Isaacs L, Geballe MT, Gilson MK. PMID: 22366955; PMCID: PMC3383923.

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   Mentions:

82  

   Fields: 

   Translation:

HumansCells

Prediction of SAMPL3 host-guest binding affinities: evaluating the accuracy of generalized force-fields. J Comput Aided Mol Des. 2012 May; 26(5):517-25. Muddana HS, Gilson MK. PMID: 22274835; PMCID: PMC3383906.

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   Mentions:

20  

   Fields: 

   Translation:

Cells

Force and Stress along Simulated Dissociation Pathways of Cucurbituril-Guest Systems. J Chem Theory Comput. 2012 Mar 13; 8(3):966-976. Velez-Vega C, Gilson MK. PMID: 22754402; PMCID: PMC3383817.

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   Mentions:

6  

   Fields: 

   

SuperTarget goes quantitative: update on drug-target interactions. Nucleic Acids Res. 2012 Jan; 40(Database issue):D1113-7. Hecker N, Ahmed J, von Eichborn J, Dunkel M, Macha K, Eckert A, Gilson MK, Bourne PE, Preissner R. PMID: 22067455; PMCID: PMC3245174.

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   Mentions:

79  

   Fields: 

   Translation:

Cells

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   Mentions:

39  

   Fields: 

   Translation:

HumansAnimals

Accelerated convergence of molecular free energy via superposition approximation-based reference states. J Chem Phys. 2011 Apr 07; 134(13):134107. Somani S, Gilson MK. PMID: 21476743; PMCID: PMC3094129.

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   Mentions:

1  

   Fields: 

   Translation:

Cells

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. J Am Chem Soc. 2011 Mar 16; 133(10):3570-81. Moghaddam S, Yang C, Rekharsky M, Ko YH, Kim K, Inoue Y, Gilson MK. PMID: 21341773; PMCID: PMC3065999.

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   Mentions:

93  

   Fields: 

   

Protein folding and binding: from biology to physics and back again. Curr Opin Struct Biol. 2011 Feb; 21(1):1-3. Gilson MK, Radford SE. PMID: 21196111; PMCID: PMC3039057.

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   Mentions:

2  

   Fields: 

   Translation:

Cells

Symmetry numbers for rigid, flexible, and fluxional molecules: theory and applications. J Phys Chem B. 2010 Dec 16; 114(49):16304-17. Gilson MK, Irikura KK. PMID: 21141931; PMCID: PMC3079527.

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   Mentions:

12  

   Fields: 

   Translation:

Cells

Modeling Protein-Ligand Binding by Mining Minima. J Chem Theory Comput. 2010 Nov 09; 6(11):3540-3557. Chen W, Gilson MK, Webb SP, Potter MJ. PMID: 22639555; PMCID: PMC3359898.

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   Mentions:

26  

   Fields: 

   

Evaluating the substrate-envelope hypothesis: structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance. J Virol. 2010 May; 84(10):5368-78. Nalam MN, Ali A, Altman MD, Reddy GS, Chellappan S, Kairys V, Ozen A, Cao H, Gilson MK, Tidor B, Rana TM, Schiffer CA. PMID: 20237088; PMCID: PMC2863851.

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   Mentions:

67  

   Fields: 

   Translation:

HumansCells

Thermodynamic and Differential Entropy under a Change of Variables. Entropy (Basel). 2010 Mar 16; 12(3):578-590. Hnizdo V, Gilson MK. PMID: 24436633; PMCID: PMC3891802.

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   Mentions:

12  

Stress Analysis at the Molecular Level: A Forced Cucurbituril-Guest Dissociation Pathway. J Chem Theory Comput. 2010 Mar 09; 6(3):637-646. Gilson MK. PMID: 23794959; PMCID: PMC3686568.

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   Mentions:

4  

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Toward the design of mutation-resistant enzyme inhibitors: further evaluation of the substrate envelope hypothesis. Chem Biol Drug Des. 2009 Sep; 74(3):234-45. Kairys V, Gilson MK, Lather V, Schiffer CA, Fernandes MX. PMID: 19703025; PMCID: PMC2860775.

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   Mentions:

10  

   Fields: 

   Translation:

HumansCells

Theory of free energy and entropy in noncovalent binding. Chem Rev. 2009 Sep; 109(9):4092-107. Zhou HX, Gilson MK. PMID: 19588959; PMCID: PMC3329805.

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   Mentions:

126  

   Fields: 

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Cells

Configurational entropy in protein-peptide binding: computational study of Tsg101 ubiquitin E2 variant domain with an HIV-derived PTAP nonapeptide. J Mol Biol. 2009 Jun 05; 389(2):315-35. Killian BJ, Kravitz JY, Somani S, Dasgupta P, Pang YP, Gilson MK. PMID: 19362095; PMCID: PMC2758778.

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   Mentions:

29  

   Fields: 

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Cells

Sampling conformations in high dimensions using low-dimensional distribution functions. J Chem Phys. 2009 Apr 07; 130(13):134102. Somani S, Killian BJ, Gilson MK. PMID: 19355712; PMCID: PMC2736589.

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   Mentions:

4  

   Fields: 

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Cells

Host-guest complexes with protein-ligand-like affinities: computational analysis and design. J Am Chem Soc. 2009 Mar 25; 131(11):4012-21. Moghaddam S, Inoue Y, Gilson MK. PMID: 19133781; PMCID: PMC2742617.

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Ions and inhibitors in the binding site of HIV protease: comparison of Monte Carlo simulations and the linearized Poisson-Boltzmann theory. Biophys J. 2009 Feb 18; 96(4):1293-306. Boda D, Valiskó M, Henderson D, Gillespie D, Eisenberg B, Gilson MK. PMID: 19217848; PMCID: PMC2717253.

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Additivity in the analysis and design of HIV protease inhibitors. J Med Chem. 2009 Feb 12; 52(3):737-54. Jorissen RN, Reddy GS, Ali A, Altman MD, Chellappan S, Anjum SG, Tidor B, Schiffer CA, Rana TM, Gilson MK. PMID: 19193159; PMCID: PMC2715819.

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Efficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methods. J Comput Chem. 2008 Jul 30; 29(10):1605-14. Hnizdo V, Tan J, Killian BJ, Gilson MK. PMID: 18293293; PMCID: PMC2620139.

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HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants. J Am Chem Soc. 2008 May 14; 130(19):6099-113. 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. PMID: 18412349; PMCID: PMC3465729.

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A synthetic host-guest system achieves avidin-biotin affinity by overcoming enthalpy-entropy compensation. Proc Natl Acad Sci U S A. 2007 Dec 26; 104(52):20737-42. 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. PMID: 18093926; PMCID: PMC2410071.

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Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol. 2007 Oct 09; 5:44. 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, Oesterheld M, Stümpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H. PMID: 17925023; PMCID: PMC2189715.

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The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol. 2007 Aug; 25(8):894-8. Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stümpflen V, Ceol A, Chatr-aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, De Las Rivas J, Prieto C, Perreau VM, Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H. PMID: 17687370.

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Extraction of configurational entropy from molecular simulations via an expansion approximation. J Chem Phys. 2007 Jul 14; 127(2):024107. Killian BJ, Yundenfreund Kravitz J, Gilson MK. PMID: 17640119; PMCID: PMC2707031.

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65  

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Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis. Chem Biol Drug Des. 2007 May; 69(5):298-313. 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. PMID: 17539822.

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Ligand configurational entropy and protein binding. Proc Natl Acad Sci U S A. 2007 Jan 30; 104(5):1534-9. Chang CE, Chen W, Gilson MK. PMID: 17242351; PMCID: PMC1780070.

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Using protein homology models for structure-based studies: approaches to model refinement. ScientificWorldJournal. 2006 Dec 06; 6:1542-54. Kairys V, Gilson MK, Fernandes MX. PMID: 17160340; PMCID: PMC5917253.

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5  

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BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res. 2007 Jan; 35(Database issue):D198-201. Liu T, Lin Y, Wen X, Jorissen RN, Gilson MK. PMID: 17145705; PMCID: PMC1751547.

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Calculation of cyclodextrin binding affinities: energy, entropy, and implications for drug design. Biophys J. 2004 Nov; 87(5):3035-49. Chen W, Chang CE, Gilson MK. PMID: 15339804; PMCID: PMC1304776.

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On the theory of noncovalent binding. Biophys J. 2004 Jul; 87(1):23-36. Mihailescu M, Gilson MK. PMID: 15240441; PMCID: PMC1304346.

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ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res. 2003 Jan 01; 31(1):147-51. Glasner JD, Liss P, Plunkett G, Darling A, Prasad T, Rusch M, Byrnes A, Gilson M, Biehl B, Blattner FR, Perna NT. PMID: 12519969; PMCID: PMC165572.

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Accelerated Poisson-Boltzmann calculations for static and dynamic systems. J Comput Chem. 2002 Oct; 23(13):1244-53. Luo R, David L, Gilson MK. PMID: 12210150.

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The physical basis of nucleic acid base stacking in water. Biophys J. 2001 Jan; 80(1):140-8. Luo R, Gilson HS, Potter MJ, Gilson MK. PMID: 11159389; PMCID: PMC1301220.

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Thermodynamic linkage between the binding of protons and inhibitors to HIV-1 protease. Protein Sci. 1999 Jan; 8(1):180-95. Trylska J, Antosiewicz J, Geller M, Hodge CN, Klabe RM, Head MS, Gilson MK. PMID: 10210196; PMCID: PMC2144115.

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The statistical-thermodynamic basis for computation of binding affinities: a critical review. Biophys J. 1997 Mar; 72(3):1047-69. Gilson MK, Given JA, Bush BL, McCammon JA. PMID: 9138555; PMCID: PMC1184492.

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The determinants of pKas in proteins. Biochemistry. 1996 Jun 18; 35(24):7819-33. Antosiewicz J, McCammon JA, Gilson MK. PMID: 8672483.

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Binding of tacrine and 6-chlorotacrine by acetylcholinesterase. Biopolymers. 1996 Jan; 38(1):109-17. Wlodek ST, Antosiewicz J, McCammon JA, Straatsma TP, Gilson MK, Briggs JM, Humblet C, Sussman JL. PMID: 8679940.

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Simulation of charge-mutant acetylcholinesterases. Biochemistry. 1995 Apr 04; 34(13):4211-9. Antosiewicz J, McCammon JA, Wlodek ST, Gilson MK. PMID: 7703233.

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Acetylcholinesterase: diffusional encounter rate constants for dumbbell models of ligand. Biophys J. 1995 Jan; 68(1):62-8. Antosiewicz J, Gilson MK, Lee IH, McCammon JA. PMID: 7711269; PMCID: PMC1281661.

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Prediction of pH-dependent properties of proteins. J Mol Biol. 1994 May 06; 238(3):415-36. Antosiewicz J, McCammon JA, Gilson MK. PMID: 8176733.

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Open "back door" in a molecular dynamics simulation of acetylcholinesterase. Science. 1994 Mar 04; 263(5151):1276-8. Gilson MK, Straatsma TP, McCammon JA, Ripoll DR, Faerman CH, Axelsen PH, Silman I, Sussman JL. PMID: 8122110.

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Destabilization of an alpha-helix-bundle protein by helix dipoles. Proc Natl Acad Sci U S A. 1989 Mar; 86(5):1524-8. Gilson MK, Honig B. PMID: 2922396; PMCID: PMC286730.

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