Michael Gilson

Title(s)Professor, School of Pharmacy and Pharmaceutical Science
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
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    AN OPEN RESOURCE TO ADVANCE COMPUTER-AIDED DRUG DESIGN
    NIH U01GM111528Sep 15, 2014 - Aug 31, 2020
    Role: Principal Investigator
    Accounting for Water Structure and Thermodynamics in Computer-Aided Drug Design
    NIH R01GM100946Sep 1, 2013 - May 31, 2022
    Role: Principal Investigator
    BindingDB: Data and Tools for Drug Discovery, Chemical Biology and Systems Pharmacology
    NIH R01GM070064Feb 1, 2004 - Dec 31, 2020
    Role: Principal Investigator
    Targeting Ensembles of Drug Resistant HIV-Protease
    NIH P01GM066524Aug 20, 2002 - Aug 31, 2013
    Role: Co-Investigator
    Theory and Modeling of Noncovalent Binding
    NIH R01GM061300Sep 1, 2000 - Aug 31, 2022
    Role: Principal Investigator
    Inexpensive Interactive Molecular Modeling Software
    NIH R42GM062050Jul 20, 2000 - Apr 30, 2006
    Role: Principal Investigator
    INEXPENSIVE, INTERACTIVE MOLECULAR MODELING SOFTWARE
    NIH R41GM062050Jul 20, 2000 - Jan 19, 2002
    Role: Principal Investigator
    Computational Anatomy and Multidimensional Modeling
    NIH P41RR013642Sep 30, 1998 - Sep 6, 2012
    Role: Co-Investigator
    THEORY OF NONCOVALENT PROTEIN-LIGAND BINDING
    NIH R29GM054053May 1, 1996 - Apr 30, 2001
    Role: Principal Investigator

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. BAT2: an Open-Source Tool for Flexible, Automated, and Low Cost Absolute Binding Free Energy Calculations. J Chem Theory Comput. 2024 Aug 01. Heinzelmann G, Huggins DJ, Gilson MK. PMID: 39088306.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    2. 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.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    3. 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.
      View in: PubMed   Mentions:    Fields:    
    4. 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.
      View in: PubMed   Mentions:    Fields:    
    5. 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.
      View in: PubMed   Mentions:    Fields:    
    6. 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.
      View in: PubMed   Mentions: 1     Fields:    
    7. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    8. 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.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    9. 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.
      View in: PubMed   Mentions:
    10. 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.
      View in: PubMed   Mentions:
    11. 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.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    12. 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.
      View in: PubMed   Mentions: 28     Fields:    
    13. 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.
      View in: PubMed   Mentions:
    14. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimals
    15. 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.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    16. 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.
      View in: PubMed   Mentions: 3  
    17. 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.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    18. 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.
      View in: PubMed   Mentions: 17     Fields:    
    19. 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.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    20. 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.
      View in: PubMed   Mentions: 11     Fields:    
    21. 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.
      View in: PubMed   Mentions: 16     Fields:    Translation:Cells
    22. 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.
      View in: PubMed   Mentions: 61     Fields:    Translation:HumansAnimalsCells
    23. Correction to Alignment-Free Antimicrobial Peptide Predictors: Improving Performance by a Thorough Analysis of the Largest Available Data Set. J Chem Inf Model. 2021 Jul 26; 61(7):3736. Pinacho-Castellanos SA, García-Jacas CR, Gilson MK, Brizuela CA. PMID: 34161087.
      View in: PubMed   Mentions:    Fields:    
    24. Alignment-Free Antimicrobial Peptide Predictors: Improving Performance by a Thorough Analysis of the Largest Available Data Set. J Chem Inf Model. 2021 06 28; 61(6):3141-3157. Pinacho-Castellanos SA, García-Jacas CR, Gilson MK, Brizuela CA. PMID: 34081438.
      View in: PubMed   Mentions: 15     Fields:    Translation:Humans
    25. 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.
      View in: PubMed   Mentions: 2     Fields:    
    26. 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.
      View in: PubMed   Mentions: 25     Fields:    Translation:Cells
    27. 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.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    28. 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.
      View in: PubMed   Mentions: 3  
    29. 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.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    30. 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.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    31. 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.
      View in: PubMed   Mentions: 34  
    32. 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.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    33. Enhanced Diffusion and Chemotaxis of Enzymes. Annu Rev Biophys. 2020 05 06; 49:87-105. Feng M, Gilson MK. PMID: 31986056.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    34. 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.
      View in: PubMed   Mentions: 40     Fields:    Translation:Cells
    35. 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.
      View in: PubMed   Mentions: 42     Fields:    Translation:Humans
    36. 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.
      View in: PubMed   Mentions: 8     Fields:    
    37. This issue: Drug Design Data Resource Grand Challenge 4, first of two issues. J Comput Aided Mol Des. 2019 12; 33(12):1009. Gilson MK. PMID: 31792883.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    38. 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.
      View in: PubMed   Mentions: 13     Fields:    
    39. 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.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimalsCells
    40. 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.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    41. 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.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    42. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    43. 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.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    44. 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.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    45. 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.
      View in: PubMed   Mentions: 63     Fields:    Translation:Cells
    46. 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.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    47. 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.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    48. 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.
      View in: PubMed   Mentions: 61     Fields:    Translation:Cells
    49. 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.
      View in: PubMed   Mentions: 66     Fields:    
    50. 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.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    51. 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.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansCells
    52. 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.
      View in: PubMed   Mentions: 12     Fields:    
    53. Motor-like Properties of Nonmotor Enzymes. Biophys J. 2018 05 08; 114(9):2174-2179. Slochower DR, Gilson MK. PMID: 29742410; PMCID: PMC5961456.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    54. Substrate-driven chemotactic assembly in an enzyme cascade. Nat Chem. 2018 03; 10(3):311-317. Zhao X, Palacci H, Yadav V, Spiering MM, Gilson MK, Butler PJ, Hess H, Benkovic SJ, Sen A. PMID: 29461522.
      View in: PubMed   Mentions: 37     Fields:    Translation:Cells
    55. 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.
      View in: PubMed   Mentions: 13     Fields:    
    56. 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.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    57. 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.
      View in: PubMed   Mentions: 84     Fields:    Translation:HumansCells
    58. 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.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    59. 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.
      View in: PubMed   Mentions: 16     Fields:    
    60. 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.
      View in: PubMed   Mentions:    Fields:    
    61. 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.
      View in: PubMed   Mentions: 34     Fields:    Translation:Cells
    62. 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.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    63. 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.
      View in: PubMed   Mentions: 3     Fields:    
    64. 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.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
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    139. 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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    140. Concepts in receptor optimization: targeting the RGD peptide. J Am Chem Soc. 2006 Apr 12; 128(14):4675-84. Chen W, Chang CE, Gilson MK. PMID: 16594704.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    141. Sensitivity Analysis and Charge-Optimization for Flexible Ligands:  Applicability to Lead Optimization. J Chem Theory Comput. 2006 Mar; 2(2):259-70. Gilson MK. PMID: 26626513.
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    142. Screening drug-like compounds by docking to homology models: a systematic study. J Chem Inf Model. 2006 Jan-Feb; 46(1):365-79. Kairys V, Fernandes MX, Gilson MK. PMID: 16426071.
      View in: PubMed   Mentions: 32     Fields:    Translation:Cells
    143. Evaluating the Accuracy of the Quasiharmonic Approximation. J Chem Theory Comput. 2005 Sep; 1(5):1017-28. Chang CE, Chen W, Gilson MK. PMID: 26641917.
      View in: PubMed   Mentions: 47     Fields:    
    144. Virtual screening of molecular databases using a support vector machine. J Chem Inf Model. 2005 May-Jun; 45(3):549-61. Jorissen RN, Gilson MK. PMID: 15921445.
      View in: PubMed   Mentions: 46     Fields:    
    145. Comparing ligand interactions with multiple receptors via serial docking. J Chem Inf Comput Sci. 2004 Nov-Dec; 44(6):1961-70. Fernandes MX, Kairys V, Gilson MK. PMID: 15554665.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    146. Free energy, entropy, and induced fit in host-guest recognition: calculations with the second-generation mining minima algorithm. J Am Chem Soc. 2004 Oct 13; 126(40):13156-64. Chang CE, Gilson MK. PMID: 15469315.
      View in: PubMed   Mentions: 84     Fields:    Translation:Cells
    147. 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.
      View in: PubMed   Mentions: 73     Fields:    Translation:Cells
    148. On the theory of noncovalent binding. Biophys J. 2004 Jul; 87(1):23-36. Mihailescu M, Gilson MK. PMID: 15240441; PMCID: PMC1304346.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    149. Identification of symmetries in molecules and complexes. J Chem Inf Comput Sci. 2004 Jul-Aug; 44(4):1301-13. Chen W, Huang J, Gilson MK. PMID: 15272838.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    150. Structural model for an AxxxG-mediated dimer of surfactant-associated protein C. Eur J Biochem. 2004 Jun; 271(11):2086-92. Kairys V, Gilson MK, Luy B. PMID: 15153098.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    151. Tork: Conformational analysis method for molecules and complexes. J Comput Chem. 2003 Dec; 24(16):1987-98. Chang CE, Gilson MK. PMID: 14531053.
      View in: PubMed   Mentions: 33     Fields:    Translation:Cells
    152. Fast assignment of accurate partial atomic charges: an electronegativity equalization method that accounts for alternate resonance forms. J Chem Inf Comput Sci. 2003 Nov-Dec; 43(6):1982-97. Gilson MK, Gilson HS, Potter MJ. PMID: 14632449.
      View in: PubMed   Mentions: 35     Fields:    
    153. Proflavine acts as a Rev inhibitor by targeting the high-affinity Rev binding site of the Rev responsive element of HIV-1. Biochemistry. 2003 Jul 08; 42(26):8035-46. DeJong ES, Chang CE, Gilson MK, Marino JP. PMID: 12834355.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCells
    154. Solution structure and functional ligand screening of HI0719, a highly conserved protein from bacteria to humans in the YjgF/YER057c/UK114 family. Biochemistry. 2003 Jan 14; 42(1):80-9. Parsons L, Bonander N, Eisenstein E, Gilson M, Kairys V, Orban J. PMID: 12515541.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansAnimalsCells
    155. 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.
      View in: PubMed   Mentions: 84     Fields:    Translation:Cells
    156. Enhanced docking with the mining minima optimizer: acceleration and side-chain flexibility. J Comput Chem. 2002 Dec; 23(16):1656-70. Kairys V, Gilson MK. PMID: 12395431.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    157. 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.
      View in: PubMed   Mentions: 161     Fields:    
    158. The bioinformatics of molecular recognition. J Mol Recognit. 2002 Jan-Feb; 15(1):1. Gilson MK. PMID: 11870915.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    159. The Binding Database: data management and interface design. Bioinformatics. 2002 Jan; 18(1):130-9. Chen X, Lin Y, Liu M, Gilson MK. PMID: 11836221.
      View in: PubMed   Mentions: 38     Fields:    Translation:Cells
    160. BindingDB: a web-accessible molecular recognition database. Comb Chem High Throughput Screen. 2001 Dec; 4(8):719-25. Chen X, Liu M, Gilson MK. PMID: 11812264.
      View in: PubMed   Mentions: 56     Fields:    Translation:Cells
    161. Interpreting trends in the binding of cyclic ureas to HIV-1 protease. J Mol Biol. 2001 Jun 01; 309(2):507-17. Mardis KL, Luo R, Gilson MK. PMID: 11371168.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    162. Ligand-receptor docking with the Mining Minima optimizer. J Comput Aided Mol Des. 2001 Feb; 15(2):157-71. David L, Luo R, Gilson MK. PMID: 11272702.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    163. 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.
      View in: PubMed   Mentions: 16     Fields:    Translation:Cells
    164. The binding database: overview and user's guide. Biopolymers. 2001-2002; 61(2):127-41. Chen X, Lin Y, Gilson MK. PMID: 11987162.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    165. Modeling molecular recognition: theory and application. J Biomol Struct Dyn. 2000; 17 Suppl 1:89-94. Mardis K, Luo R, David L, Potter M, Glemza A, Payne G, Gilson MK. PMID: 22607411.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    166. Nucleic acid base-pairing and N-methylacetamide self-association in chloroform: affinity and conformation. Biophys Chem. 1999 Apr 05; 78(1-2):183-93. Luo R, Head MS, Given JA, Gilson MK. PMID: 10343387.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    167. 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.
      View in: PubMed   Mentions: 17     Fields:    
    168. A hierarchical method for generating low-energy conformers of a protein-ligand complex. Proteins. 1998 Dec 01; 33(4):475-95. Given JA, Gilson MK. PMID: 9849934.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    169. Theoretical and experimental analysis of ionization equilibria in ovomucoid third domain. Biochemistry. 1998 Jun 16; 37(24):8643-52. Forsyth WR, Gilson MK, Antosiewicz J, Jaren OR, Robertson AD. PMID: 9628726.
      View in: PubMed   Mentions: 16     Fields:    Translation:Cells
    170. pKa 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. 1997 Mar 25; 36(12):3580-9. Khare D, Alexander P, Antosiewicz J, Bryan P, Gilson M, Orban J. PMID: 9132009.
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    171. 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.
      View in: PubMed   Mentions: 381     Fields:    Translation:Cells
    172. A new class of models for computing receptor-ligand binding affinities. Chem Biol. 1997 Feb; 4(2):87-92. Gilson MK, Given JA, Head MS. PMID: 9190290.
      View in: PubMed   Mentions: 18     Fields:    
    173. The determinants of pKas in proteins. Biochemistry. 1996 Jun 18; 35(24):7819-33. Antosiewicz J, McCammon JA, Gilson MK. PMID: 8672483.
      View in: PubMed   Mentions: 133     Fields:    Translation:Cells
    174. 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.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    175. Simulation of charge-mutant acetylcholinesterases. Biochemistry. 1995 Apr 04; 34(13):4211-9. Antosiewicz J, McCammon JA, Wlodek ST, Gilson MK. PMID: 7703233.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansAnimalsCells
    176. Theory of electrostatic interactions in macromolecules. Curr Opin Struct Biol. 1995 Apr; 5(2):216-23. Gilson MK. PMID: 7648324.
      View in: PubMed   Mentions: 66     Fields:    Translation:Cells
    177. 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.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    178. 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.
      View in: PubMed   Mentions: 206     Fields:    Translation:Cells
    179. 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.
      View in: PubMed   Mentions: 63     Fields:    Translation:Cells
    180. Multiple-site titration and molecular modeling: two rapid methods for computing energies and forces for ionizable groups in proteins. Proteins. 1993 Mar; 15(3):266-82. Gilson MK. PMID: 8456096.
      View in: PubMed   Mentions: 79     Fields:    Translation:AnimalsCells
    181. The inclusion of electrostatic hydration energies in molecular mechanics calculations. J Comput Aided Mol Des. 1991 Feb; 5(1):5-20. Gilson MK, Honig B. PMID: 2072125.
      View in: PubMed   Mentions: 27     Fields:    Translation:Cells
    182. 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.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    183. Electrostatic interactions in proteins. Prog Clin Biol Res. 1989; 289:65-74. Honig B, Sharp K, Gilson M. PMID: 2726810.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    184. Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis. Proteins. 1988; 4(1):7-18. Gilson MK, Honig B. PMID: 3186692.
      View in: PubMed   Mentions: 180     Fields:    Translation:Cells
    185. Energetics of charge-charge interactions in proteins. Proteins. 1988; 3(1):32-52. Gilson MK, Honig BH. PMID: 3287370.
      View in: PubMed   Mentions: 67     Fields:    Translation:Cells
    186. Calculation of electrostatic potentials in an enzyme active site. Nature. 1987 Nov 5-11; 330(6143):84-6. Gilson MK, Honig BH. PMID: 3313058.
      View in: PubMed   Mentions: 82     Fields:    Translation:Cells
    187. The dielectric constant of a folded protein. Biopolymers. 1986 Nov; 25(11):2097-119. Gilson MK, Honig BH. PMID: 3790703.
      View in: PubMed   Mentions: 98     Fields:    Translation:Cells
    188. On the calculation of electrostatic interactions in proteins. J Mol Biol. 1985 Aug 05; 184(3):503-16. Gilson MK, Rashin A, Fine R, Honig B. PMID: 4046024.
      View in: PubMed   Mentions: 59     Fields:    Translation:Cells
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