Loading...

Michael K Gilson

Title(s)Professor and Chair in Computer-Aided Drug Design, School of Pharmacy and Pharmaceutical Science
SchoolHealth Sciences
Phone858-822-0622
vCardDownload vCard

    Collapse Research 
    Collapse Research Activities and Funding
    AN OPEN RESOURCE TO ADVANCE COMPUTER-AIDED DRUG DESIGN
    NIH/NIGMS U01GM111528Sep 15, 2014 - Aug 31, 2019
    Role: Principal Investigator
    Accounting for Water Structure and Thermodynamics in Computer-Aided Drug Design
    NIH/NIGMS R01GM100946Sep 1, 2013 - May 31, 2022
    Role: Principal Investigator
    BindingDB: Data and Tools for Drug Discovery, Chemical Biology and Systems Pharmacology
    NIH/NIGMS 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/NIGMS R01GM061300Sep 1, 2000 - Aug 31, 2022
    Role: Principal Investigator
    Inexpensive Interactive Molecular Modeling Software
    NIH/NIGMS R42GM062050Jul 20, 2000 - Apr 30, 2006
    Role: Principal Investigator
    INEXPENSIVE, INTERACTIVE MOLECULAR MODELING SOFTWARE
    NIH/NIGMS R41GM062050Jul 20, 2000 - Jan 19, 2002
    Role: Principal Investigator
    Computational Anatomy and Multidimensional Modeling
    NIH/NCRR P41RR013642Sep 30, 1998 - Sep 6, 2012
    Role: Co-Investigator
    THEORY OF NONCOVALENT PROTEIN-LIGAND BINDING
    NIH/NIGMS R29GM054053May 1, 1996 - Apr 30, 2001
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Websites

    Collapse Bibliographic 
    Collapse Publications
    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.
    List All   |   Timeline
    1. 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. Antitumor Activity of 1,18-Octadecanedioic Acid-Paclitaxel Complexed with Human Serum Albumin. J Am Chem Soc. 2019 Jul 18. PMID: 31317744.
      View in: PubMed
    2. 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. 2019; 14(7):e0219473. PMID: 31291328.
      View in: PubMed
    3. 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. 2019 Jun 24. PMID: 31257108.
      View in: PubMed
    4. 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. Entropic effects enable life at extreme temperatures. Sci Adv. 2019 May; 5(5):eaaw4783. PMID: 31049402.
      View in: PubMed
    5. Feng M, Gilson MK. A Thermodynamic Limit on the Role of Self-Propulsion in Enhanced Enzyme Diffusion. Biophys J. 2019 May 21; 116(10):1898-1906. PMID: 31053258.
      View in: PubMed
    6. Ben-Shalom IY, Lin C, Kurtzman T, Walker RC, Gilson MK. Simulating Water Exchange to Buried Binding Sites. J Chem Theory Comput. 2019 Apr 09; 15(4):2684-2691. PMID: 30835999.
      View in: PubMed
    7. 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. J Comput Aided Mol Des. 2019 Jan; 33(1):1-18. PMID: 30632055.
      View in: PubMed
    8. 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. J Chem Theory Comput. 2019 Jan 08; 15(1):402-423. PMID: 30512951.
      View in: PubMed
    9. Tallorin L, Wang J, Kim WE, Sahu S, Kosa NM, Yang P, Thompson M, Gilson MK, Frazier PI, Burkart MD, Gianneschi NC. Discovering de novo peptide substrates for enzymes using machine learning. Nat Commun. 2018 12 07; 9(1):5253. PMID: 30531862.
      View in: PubMed
    10. 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. J Comput Aided Mol Des. 2018 Oct; 32(10):937-963. PMID: 30415285.
      View in: PubMed
    11. Mobley DL, Bannan CC, Rizzi A, Bayly CI, Chodera JD, Lim VT, Lim NM, Beauchamp KA, Slochower DR, Shirts MR, Gilson MK, Eastman PK. Escaping Atom Types in Force Fields Using Direct Chemical Perception. J Chem Theory Comput. 2018 Nov 13; 14(11):6076-6092. PMID: 30351006.
      View in: PubMed
    12. Li A, Gilson MK. Protein-ligand binding enthalpies from near-millisecond simulations: Analysis of a preorganization paradox. J Chem Phys. 2018 Aug 21; 149(7):072311. PMID: 30134726.
      View in: PubMed
    13. Chen SF, Huang NL, Lin JH, Wu CC, Wang YR, Yu YJ, Gilson MK, Chan NL. Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate. Nat Commun. 2018 08 06; 9(1):3085. PMID: 30082834.
      View in: PubMed
    14. Yin J, Henriksen NM, Muddana HS, Gilson MK. Bind3P: Optimization of a Water Model Based on Host-Guest Binding Data. J Chem Theory Comput. 2018 Jul 10; 14(7):3621-3632. PMID: 29874074.
      View in: PubMed
    15. Slochower DR, Gilson MK. Motor-like Properties of Nonmotor Enzymes. Biophys J. 2018 May 08; 114(9):2174-2179. PMID: 29742410.
      View in: PubMed
    16. Zhao X, Palacci H, Yadav V, Spiering MM, Gilson MK, Butler PJ, Hess H, Benkovic SJ, Sen A. Substrate-driven chemotactic assembly in an enzyme cascade. Nat Chem. 2018 Mar; 10(3):311-317. PMID: 29461522.
      View in: PubMed
    17. 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. J Chem Theory Comput. 2018 Jan 09; 14(1):418-425. PMID: 29161510.
      View in: PubMed
    18. Kantonen SA, Henriksen NM, Gilson MK. Accounting for apparent deviations between calorimetric and van't Hoff enthalpies. Biochim Biophys Acta Gen Subj. 2018 Mar; 1862(3):692-704. PMID: 29221984.
      View in: PubMed
    19. 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. J Comput Aided Mol Des. 2018 01; 32(1):1-20. PMID: 29204945.
      View in: PubMed
    20. Assaf KI, Florea M, Antony J, Henriksen NM, Yin J, Hansen A, Qu ZW, Sure R, Klapstein D, Gilson MK, Grimme S, Nau WM. 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. PMID: 29140701.
      View in: PubMed
    21. 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. J Chem Theory Comput. 2017 Sep 12; 13(9):4253-4269. PMID: 28696692.
      View in: PubMed
    22. Shirts MR, Klein C, Swails JM, Yin J, Gilson MK, Mobley DL, Case DA, Zhong ED. Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. J Comput Aided Mol Des. 2017 08; 31(8):777. PMID: 28752343.
      View in: PubMed
    23. 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. Proc Natl Acad Sci U S A. 2017 08 15; 114(33):E6839-E6846. PMID: 28760952.
      View in: PubMed
    24. Heinzelmann G, Henriksen NM, Gilson MK. 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. PMID: 28564537.
      View in: PubMed
    25. Reany O, Li A, Yefet M, Gilson MK, Keinan E. Attractive Interactions between Heteroallenes and the Cucurbituril Portal. J Am Chem Soc. 2017 06 21; 139(24):8138-8145. PMID: 28532152.
      View in: PubMed
    26. Chabolla SA, Machan CW, Yin J, Dellamary EA, Sahu S, Gianneschi NC, Gilson MK, Tezcan FA, Kubiak CP. 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. PMID: 28374024.
      View in: PubMed
    27. Mobley DL, Gilson MK. Predicting Binding Free Energies: Frontiers and Benchmarks. Annu Rev Biophys. 2017 05 22; 46:531-558. PMID: 28399632.
      View in: PubMed
    28. 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. Arch Biochem Biophys. 2017 Jan 01; 613:1-11. PMID: 27983948.
      View in: PubMed
    29. 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. J Comput Aided Mol Des. 2017 01; 31(1):147-161. PMID: 27787702.
      View in: PubMed
    30. 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. J Comput Aided Mol Des. 2016 09; 30(9):651-668. PMID: 27696240.
      View in: PubMed
    31. Bannan CC, Burley KH, Chiu M, Shirts MR, Gilson MK, Mobley DL. Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge. J Comput Aided Mol Des. 2016 11; 30(11):927-944. PMID: 27677750.
      View in: PubMed
    32. 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? J Comput Aided Mol Des. 2017 01; 31(1):1-19. PMID: 27658802.
      View in: PubMed
    33. 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. J Comput Aided Mol Des. 2017 01; 31(1):133-145. PMID: 27638809.
      View in: PubMed
    34. Kantonen SA, Henriksen NM, Gilson MK. 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. PMID: 27599357.
      View in: PubMed
    35. Muddana HS, Sapra NV, Fenley AT, Gilson MK. 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 Jul 28; 145(4):049902. PMID: 27475401.
      View in: PubMed
    36. 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. J Am Chem Soc. 2016 07 06; 138(26):8184-93. PMID: 27258781.
      View in: PubMed
    37. Ramsey S, Nguyen C, Salomon-Ferrer R, Walker RC, Gilson MK, Kurtzman T. Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST. J Comput Chem. 2016 08 05; 37(21):2029-37. PMID: 27317094.
      View in: PubMed
    38. Li A, Voronin A, Fenley AT, Gilson MK. Evaluation of Representations and Response Models for Polarizable Force Fields. J Phys Chem B. 2016 08 25; 120(33):8668-84. PMID: 27248842.
      View in: PubMed
    39. Haider K, Wickstrom L, Ramsey S, Gilson MK, Kurtzman T. Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces. J Phys Chem B. 2016 09 01; 120(34):8743-56. PMID: 27169482.
      View in: PubMed
    40. Nguyen CN, Kurtzman T, Gilson MK. Spatial Decomposition of Translational Water-Water Correlation Entropy in Binding Pockets. J Chem Theory Comput. 2016 Jan 12; 12(1):414-29. PMID: 26636620; PMCID: PMC4819442 [Available on 01/12/17].
    41. 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 Res. 2016 Jan 04; 44(D1):D1045-53. PMID: 26481362; PMCID: PMC4702793.
    42. 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. J Chem Theory Comput. 2015 Oct 13; 11(10):4555-64. PMID: 26574247.
      View in: PubMed
    43. Nicola G, Berthold MR, Hedrick MP, Gilson MK. Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME. Database (Oxford). 2015; 2015. PMID: 26384374; PMCID: PMC4572361.
    44. Henriksen NM, Fenley AT, Gilson MK. Computational Calorimetry: High-Precision Calculation of Host-Guest Binding Thermodynamics. J Chem Theory Comput. 2015 Sep 08; 11(9):4377-94. PMID: 26523125; PMCID: PMC4614838.
    45. 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. J Mol Recognit. 2016 Jan; 29(1):10-21. PMID: 26256816; PMCID: PMC4715590.
    46. Yin J, Fenley AT, Henriksen NM, Gilson MK. Toward Improved Force-Field Accuracy through Sensitivity Analysis of Host-Guest Binding Thermodynamics. J Phys Chem B. 2015 Aug 13; 119(32):10145-55. PMID: 26181208.
      View in: PubMed
    47. Fenley AT, Muddana HS, Gilson MK. Calculation and visualization of atomistic mechanical stresses in nanomaterials and biomolecules. PLoS One. 2014; 9(12):e113119. PMID: 25503996.
      View in: PubMed
    48. McClendon CL, Kornev AP, Gilson MK, Taylor SS. Dynamic architecture of a protein kinase. Proc Natl Acad Sci U S A. 2014 Oct 28; 111(43):E4623-31. PMID: 25319261; PMCID: PMC4217441.
    49. Blum AP, Kammeyer JK, Yin J, Crystal DT, Rush AM, Gilson MK, Gianneschi NC. Peptides displayed as high density brush polymers resist proteolysis and retain bioactivity. J Am Chem Soc. 2014 Oct 29; 136(43):15422-37. PMID: 25314576.
      View in: PubMed
    50. Machan CW, Chabolla SA, Yin J, Gilson MK, Tezcan FA, Kubiak CP. 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. PMID: 25226161.
      View in: PubMed
    51. Fenley AT, Henriksen NM, Muddana HS, Gilson MK. Bridging Calorimetry and Simulation through Precise Calculations of Cucurbituril-Guest Binding Enthalpies. J Chem Theory Comput. 2014 Sep 09; 10(9):4069-4078. PMID: 25221445.
      View in: PubMed
    52. Fenley AT, Killian BJ, Hnizdo V, Fedorowicz A, Sharp DS, Gilson MK. Correlation as a determinant of configurational entropy in supramolecular and protein systems. J Phys Chem B. 2014 Jun 19; 118(24):6447-55. PMID: 24702693; PMCID: PMC4067153.
    53. Nguyen CN, Cruz A, Gilson MK, Kurtzman T. 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. PMID: 25018673.
      View in: PubMed
    54. Muddana HS, Fenley AT, Mobley DL, Gilson MK. The SAMPL4 host-guest blind prediction challenge: an overview. J Comput Aided Mol Des. 2014 Apr; 28(4):305-17. PMID: 24599514; PMCID: PMC4053502.
    55. Li A, Muddana HS, Gilson MK. 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. PMID: 24803867.
      View in: PubMed
    56. Gilson MK, Georg G, Wang S. Digital chemistry in the Journal of Medicinal Chemistry. J Med Chem. 2014 Feb 27; 57(4):1137. PMID: 24521446.
      View in: PubMed
    57. Muddana HS, Yin J, Sapra NV, Fenley AT, Gilson MK. 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. PMID: 24510191; PMCID: PMC4053532.
    58. Muddana HS, Sapra NV, Fenley AT, Gilson MK. 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. PMID: 24477800; PMCID: PMC4006311.
    59. Velez-Vega C, Gilson MK. Overcoming dissipation in the calculation of standard binding free energies by ligand extraction. J Comput Chem. 2013 Oct 15; 34(27):2360-71. PMID: 24038118; PMCID: PMC3932244.
    60. Muddana HS, Sapra NV, Fenley AT, Gilson MK. The electrostatic response of water to neutral polar solutes: implications for continuum solvent modeling. J Chem Phys. 2013 Jun 14; 138(22):224504. PMID: 23781802; PMCID: PMC3695974.
    61. Fenley AT, Muddana HS, Gilson MK. 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. PMID: 23150595; PMCID: PMC3523842.
    62. Orchard S, Binz PA, Borchers C, Gilson MK, Jones AR, Nicola G, Vizcaino JA, Deutsch EW, Hermjakob H. 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. PMID: 22969026; PMCID: PMC3895333.
    63. Nguyen CN, Young TK, Gilson MK. Grid inhomogeneous solvation theory: hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril. J Chem Phys. 2012 Jul 28; 137(4):044101. PMID: 22852591; PMCID: PMC3416872.
    64. Nicola G, Liu T, Gilson MK. Public domain databases for medicinal chemistry. J Med Chem. 2012 Aug 23; 55(16):6987-7002. PMID: 22731701; PMCID: PMC3427776.
    65. Shen Y, Gilson MK, Tidor B. Charge Optimization Theory for Induced-Fit Ligands. J Chem Theory Comput. 2012 Nov 13; 8(11):4580-4592. PMID: 23162383.
      View in: PubMed
    66. Forrey C, Douglas JF, Gilson MK. The Fundamental Role of Flexibility on the Strength of Molecular Binding. Soft Matter. 2012; 8(23):6385-6392. PMID: 22707976.
      View in: PubMed
    67. Muddana HS, Gilson MK. Calculation of Host-Guest Binding Affinities Using a Quantum-Mechanical Energy Model. J Chem Theory Comput. 2012 Jun 12; 8(6):2023-2033. PMID: 22737045.
      View in: PubMed
    68. Pereira AR, Kale AJ, Fenley AT, Byrum T, Debonsi HM, Gilson MK, Valeriote FA, Moore BS, Gerwick WH. The carmaphycins: new proteasome inhibitors exhibiting an a,ß-epoxyketone warhead from a marine cyanobacterium. Chembiochem. 2012 Apr 16; 13(6):810-7. PMID: 22383253; PMCID: PMC3393770.
    69. 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. J Comput Aided Mol Des. 2012 May; 26(5):475-87. PMID: 22366955; PMCID: PMC3383923.
    70. Muddana HS, Gilson MK. 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. PMID: 22274835.
      View in: PubMed
    71. Velez-Vega C, Gilson MK. Force and Stress along Simulated Dissociation Pathways of Cucurbituril-Guest Systems. J Chem Theory Comput. 2012 Mar 13; 8(3):966-976. PMID: 22754402.
      View in: PubMed
    72. Hecker N, Ahmed J, von Eichborn J, Dunkel M, Macha K, Eckert A, Gilson MK, Bourne PE, Preissner R. SuperTarget goes quantitative: update on drug-target interactions. Nucleic Acids Res. 2012 Jan; 40(Database issue):D1113-7. PMID: 22067455; PMCID: PMC3245174.
    73. 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, Larminie C, Lynch N, Mann RK, Murray-Rust P, Lo Piparo E, Southan C, Steinbeck C, Wishart D, Hermjakob H, Overington J, Thornton J. Minimum information about a bioactive entity (MIABE). Nat Rev Drug Discov. 2011 Aug 31; 10(9):661-9. PMID: 21878981.
      View in: PubMed
    74. Somani S, Gilson MK. Accelerated convergence of molecular free energy via superposition approximation-based reference states. J Chem Phys. 2011 Apr 07; 134(13):134107. PMID: 21476743; PMCID: PMC3094129.
    75. 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. J Am Chem Soc. 2011 Mar 16; 133(10):3570-81. PMID: 21341773; PMCID: PMC3065999.
    76. Gilson MK, Radford SE. Protein folding and binding: from biology to physics and back again. Curr Opin Struct Biol. 2011 Feb; 21(1):1-3. PMID: 21196111; PMCID: PMC3039057.
    77. Gilson MK, Irikura KK. Symmetry numbers for rigid, flexible, and fluxional molecules: theory and applications. J Phys Chem B. 2010 Dec 16; 114(49):16304-17. PMID: 21141931; PMCID: PMC3079527.
    78. Chen W, Gilson MK, Webb SP, Potter MJ. Modeling Protein-Ligand Binding by Mining Minima. J Chem Theory Comput. 2010 Nov 09; 6(11):3540-3557. PMID: 22639555.
      View in: PubMed
    79. 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. J Virol. 2010 May; 84(10):5368-78. PMID: 20237088; PMCID: PMC2863851.
    80. Hnizdo V, Gilson MK. Thermodynamic and Differential Entropy under a Change of Variables. Entropy (Basel). 2010 Mar 16; 12(3):578-590. PMID: 24436633.
      View in: PubMed
    81. Gilson MK. Stress Analysis at the Molecular Level: A Forced Cucurbituril-Guest Dissociation Pathway. J Chem Theory Comput. 2010 Mar 09; 6(3):637-646. PMID: 23794959.
      View in: PubMed
    82. Kairys V, Gilson MK, Lather V, Schiffer CA, Fernandes MX. 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. PMID: 19703025; PMCID: PMC2860775.
    83. Zhou HX, Gilson MK. Theory of free energy and entropy in noncovalent binding. Chem Rev. 2009 Sep; 109(9):4092-107. PMID: 19588959; PMCID: PMC3329805.
    84. 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. J Mol Biol. 2009 Jun 05; 389(2):315-35. PMID: 19362095; PMCID: PMC2758778.
    85. Somani S, Killian BJ, Gilson MK. Sampling conformations in high dimensions using low-dimensional distribution functions. J Chem Phys. 2009 Apr 07; 130(13):134102. PMID: 19355712; PMCID: PMC2736589.
    86. Moghaddam S, Inoue Y, Gilson MK. Host-guest complexes with protein-ligand-like affinities: computational analysis and design. J Am Chem Soc. 2009 Mar 25; 131(11):4012-21. PMID: 19133781; PMCID: PMC2742617.
    87. 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. Biophys J. 2009 Feb 18; 96(4):1293-306. PMID: 19217848; PMCID: PMC2717253.
    88. 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. J Med Chem. 2009 Feb 12; 52(3):737-54. PMID: 19193159; PMCID: PMC2715819.
    89. 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. J Comput Chem. 2008 Jul 30; 29(10):1605-14. PMID: 18293293.
      View in: PubMed
    90. 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. J Am Chem Soc. 2008 May 14; 130(19):6099-113. PMID: 18412349.
      View in: PubMed
    91. 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. Proc Natl Acad Sci U S A. 2007 Dec 26; 104(52):20737-42. PMID: 18093926; PMCID: PMC2410071.
    92. 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. Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol. 2007 Oct 09; 5:44. PMID: 17925023; PMCID: PMC2189715.
    93. Chellappan S, Kairys V, Fernandes MX, Schiffer C, Gilson MK. Evaluation of the substrate envelope hypothesis for inhibitors of HIV-1 protease. Proteins. 2007 Aug 01; 68(2):561-7. PMID: 17474129.
      View in: PubMed
    94. 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. The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol. 2007 Aug; 25(8):894-8. PMID: 17687370.
      View in: PubMed
    95. Killian BJ, Yundenfreund Kravitz J, Gilson MK. Extraction of configurational entropy from molecular simulations via an expansion approximation. J Chem Phys. 2007 Jul 14; 127(2):024107. PMID: 17640119.
      View in: PubMed
    96. 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. Chem Biol Drug Des. 2007 May; 69(5):298-313. PMID: 17539822.
      View in: PubMed
    97. Chen W, Gilson MK. ConCept: de novo design of synthetic receptors for targeted ligands. J Chem Inf Model. 2007 Mar-Apr; 47(2):425-34. PMID: 17315861.
      View in: PubMed
    98. Chang CE, Chen W, Gilson MK. Ligand configurational entropy and protein binding. Proc Natl Acad Sci U S A. 2007 Jan 30; 104(5):1534-9. PMID: 17242351.
      View in: PubMed
    99. Gilson MK, Zhou HX. Calculation of protein-ligand binding affinities. Annu Rev Biophys Biomol Struct. 2007; 36:21-42. PMID: 17201676.
      View in: PubMed
    100. Kairys V, Gilson MK, Fernandes MX. Using protein homology models for structure-based studies: approaches to model refinement. ScientificWorldJournal. 2006 Dec 06; 6:1542-54. PMID: 17160340.
      View in: PubMed
    101. Liu T, Lin Y, Wen X, Jorissen RN, Gilson MK. BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res. 2007 Jan; 35(Database issue):D198-201. PMID: 17145705; PMCID: PMC1751547.
    102. Chen W, Chang CE, Gilson MK. Concepts in receptor optimization: targeting the RGD peptide. J Am Chem Soc. 2006 Apr 12; 128(14):4675-84. PMID: 16594704.
      View in: PubMed
    103. Gilson MK. Sensitivity Analysis and Charge-Optimization for Flexible Ligands:? Applicability to Lead Optimization. J Chem Theory Comput. 2006 Mar; 2(2):259-70. PMID: 26626513.
      View in: PubMed
    104. Kairys V, Fernandes MX, Gilson MK. Screening drug-like compounds by docking to homology models: a systematic study. J Chem Inf Model. 2006 Jan-Feb; 46(1):365-79. PMID: 16426071.
      View in: PubMed
    105. Chang CE, Chen W, Gilson MK. Evaluating the Accuracy of the Quasiharmonic Approximation. J Chem Theory Comput. 2005 Sep; 1(5):1017-28. PMID: 26641917.
      View in: PubMed
    106. Jorissen RN, Gilson MK. Virtual screening of molecular databases using a support vector machine. J Chem Inf Model. 2005 May-Jun; 45(3):549-61. PMID: 15921445.
      View in: PubMed
    107. Fernandes MX, Kairys V, Gilson MK. Comparing ligand interactions with multiple receptors via serial docking. J Chem Inf Comput Sci. 2004 Nov-Dec; 44(6):1961-70. PMID: 15554665.
      View in: PubMed
    108. Chang CE, Gilson MK. 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. PMID: 15469315.
      View in: PubMed
    109. Chen W, Chang CE, Gilson MK. Calculation of cyclodextrin binding affinities: energy, entropy, and implications for drug design. Biophys J. 2004 Nov; 87(5):3035-49. PMID: 15339804; PMCID: PMC1304776.
    110. Mihailescu M, Gilson MK. On the theory of noncovalent binding. Biophys J. 2004 Jul; 87(1):23-36. PMID: 15240441; PMCID: PMC1304346.
    111. Chen W, Huang J, Gilson MK. Identification of symmetries in molecules and complexes. J Chem Inf Comput Sci. 2004 Jul-Aug; 44(4):1301-13. PMID: 15272838.
      View in: PubMed
    112. Kairys V, Gilson MK, Luy B. Structural model for an AxxxG-mediated dimer of surfactant-associated protein C. Eur J Biochem. 2004 Jun; 271(11):2086-92. PMID: 15153098.
      View in: PubMed
    113. Chang CE, Gilson MK. Tork: Conformational analysis method for molecules and complexes. J Comput Chem. 2003 Dec; 24(16):1987-98. PMID: 14531053.
      View in: PubMed
    114. Gilson MK, Gilson HS, Potter MJ. 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. PMID: 14632449.
      View in: PubMed
    115. 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. 2003 Jul 08; 42(26):8035-46. PMID: 12834355.
      View in: PubMed
    116. 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. 2003 Jan 14; 42(1):80-9. PMID: 12515541.
      View in: PubMed
    117. Glasner JD, Liss P, Plunkett G, Darling A, Prasad T, Rusch M, Byrnes A, Gilson M, Biehl B, Blattner FR, Perna NT. ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res. 2003 Jan 01; 31(1):147-51. PMID: 12519969; PMCID: PMC165572.
    118. Kairys V, Gilson MK. Enhanced docking with the mining minima optimizer: acceleration and side-chain flexibility. J Comput Chem. 2002 Dec; 23(16):1656-70. PMID: 12395431.
      View in: PubMed
    119. Luo R, David L, Gilson MK. Accelerated Poisson-Boltzmann calculations for static and dynamic systems. J Comput Chem. 2002 Oct; 23(13):1244-53. PMID: 12210150.
      View in: PubMed
    120. Chen X, Lin Y, Liu M, Gilson MK. The Binding Database: data management and interface design. Bioinformatics. 2002 Jan; 18(1):130-9. PMID: 11836221.
      View in: PubMed
    121. Gilson MK. The bioinformatics of molecular recognition. J Mol Recognit. 2002 Jan-Feb; 15(1):1. PMID: 11870915.
      View in: PubMed
    122. Chen X, Liu M, Gilson MK. BindingDB: a web-accessible molecular recognition database. Comb Chem High Throughput Screen. 2001 Dec; 4(8):719-25. PMID: 11812264.
      View in: PubMed
    123. Mardis KL, Luo R, Gilson MK. Interpreting trends in the binding of cyclic ureas to HIV-1 protease. J Mol Biol. 2001 Jun 01; 309(2):507-17. PMID: 11371168.
      View in: PubMed
    124. David L, Luo R, Gilson MK. Ligand-receptor docking with the Mining Minima optimizer. J Comput Aided Mol Des. 2001 Feb; 15(2):157-71. PMID: 11272702.
      View in: PubMed
    125. Luo R, Gilson HS, Potter MJ, Gilson MK. The physical basis of nucleic acid base stacking in water. Biophys J. 2001 Jan; 80(1):140-8. PMID: 11159389.
      View in: PubMed
    126. Chen X, Lin Y, Gilson MK. The binding database: overview and user's guide. Biopolymers. 2001-2002; 61(2):127-41. PMID: 11987162.
      View in: PubMed
    127. Mardis K, Luo R, David L, Potter M, Glemza A, Payne G, Gilson MK. Modeling molecular recognition: theory and application. J Biomol Struct Dyn. 2000; 17 Suppl 1:89-94. PMID: 22607411.
      View in: PubMed
    128. Luo R, Head MS, Given JA, Gilson MK. Nucleic acid base-pairing and N-methylacetamide self-association in chloroform: affinity and conformation. Biophys Chem. 1999 Apr 05; 78(1-2):183-93. PMID: 10343387.
      View in: PubMed
    129. Trylska J, Antosiewicz J, Geller M, Hodge CN, Klabe RM, Head MS, Gilson MK. Thermodynamic linkage between the binding of protons and inhibitors to HIV-1 protease. Protein Sci. 1999 Jan; 8(1):180-95. PMID: 10210196.
      View in: PubMed
    130. Given JA, Gilson MK. A hierarchical method for generating low-energy conformers of a protein-ligand complex. Proteins. 1998 Dec 01; 33(4):475-95. PMID: 9849934.
      View in: PubMed
    131. Forsyth WR, Gilson MK, Antosiewicz J, Jaren OR, Robertson AD. Theoretical and experimental analysis of ionization equilibria in ovomucoid third domain. Biochemistry. 1998 Jun 16; 37(24):8643-52. PMID: 9628726.
      View in: PubMed
    132. Khare D, Alexander P, Antosiewicz J, Bryan P, Gilson M, Orban J. 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. PMID: 9132009.
      View in: PubMed
    133. Gilson MK, Given JA, Bush BL, McCammon JA. The statistical-thermodynamic basis for computation of binding affinities: a critical review. Biophys J. 1997 Mar; 72(3):1047-69. PMID: 9138555.
      View in: PubMed
    134. Gilson MK, Given JA, Head MS. A new class of models for computing receptor-ligand binding affinities. Chem Biol. 1997 Feb; 4(2):87-92. PMID: 9190290.
      View in: PubMed
    135. Antosiewicz J, McCammon JA, Gilson MK. The determinants of pKas in proteins. Biochemistry. 1996 Jun 18; 35(24):7819-33. PMID: 8672483.
      View in: PubMed
    136. 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. 1996 Jan; 38(1):109-17. PMID: 8679940.
      View in: PubMed
    137. Antosiewicz J, McCammon JA, Wlodek ST, Gilson MK. Simulation of charge-mutant acetylcholinesterases. Biochemistry. 1995 Apr 04; 34(13):4211-9. PMID: 7703233.
      View in: PubMed
    138. Gilson MK. Theory of electrostatic interactions in macromolecules. Curr Opin Struct Biol. 1995 Apr; 5(2):216-23. PMID: 7648324.
      View in: PubMed
    139. Antosiewicz J, Gilson MK, Lee IH, McCammon JA. Acetylcholinesterase: diffusional encounter rate constants for dumbbell models of ligand. Biophys J. 1995 Jan; 68(1):62-8. PMID: 7711269.
      View in: PubMed
    140. Antosiewicz J, McCammon JA, Gilson MK. Prediction of pH-dependent properties of proteins. J Mol Biol. 1994 May 06; 238(3):415-36. PMID: 8176733.
      View in: PubMed
    141. 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. 1994 Mar 04; 263(5151):1276-8. PMID: 8122110.
      View in: PubMed
    142. Gilson MK. 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. PMID: 8456096.
      View in: PubMed
    143. Gilson MK, Honig B. The inclusion of electrostatic hydration energies in molecular mechanics calculations. J Comput Aided Mol Des. 1991 Feb; 5(1):5-20. PMID: 2072125.
      View in: PubMed
    144. Gilson MK, Honig B. Destabilization of an alpha-helix-bundle protein by helix dipoles. Proc Natl Acad Sci U S A. 1989 Mar; 86(5):1524-8. PMID: 2922396.
      View in: PubMed
    145. Honig B, Sharp K, Gilson M. Electrostatic interactions in proteins. Prog Clin Biol Res. 1989; 289:65-74. PMID: 2726810.
      View in: PubMed
    146. Gilson MK, Honig BH. Energetics of charge-charge interactions in proteins. Proteins. 1988; 3(1):32-52. PMID: 3287370.
      View in: PubMed
    147. Gilson MK, Honig B. Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis. Proteins. 1988; 4(1):7-18. PMID: 3186692.
      View in: PubMed
    148. Gilson MK, Honig BH. Calculation of electrostatic potentials in an enzyme active site. Nature. 1987 Nov 5-11; 330(6143):84-6. PMID: 3313058.
      View in: PubMed
    149. Gilson MK, Honig BH. The dielectric constant of a folded protein. Biopolymers. 1986 Nov; 25(11):2097-119. PMID: 3790703.
      View in: PubMed
    150. Gilson MK, Rashin A, Fine R, Honig B. On the calculation of electrostatic interactions in proteins. J Mol Biol. 1985 Aug 05; 184(3):503-16. PMID: 4046024.
      View in: PubMed