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    Michael Gilson

    TitleProfessor and Chair in Computer-Aided Drug Design
    SchoolUniversity of California, San Diego
    DepartmentCenter for Drug Discovery
    Address9500 Gilman Drive #0736
    CA La Jolla 92093
    Phone858-822-0622
    vCardDownload vCard

      Collapse Research 
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      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 - Apr 30, 2017
      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, 2018
      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 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 
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      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.
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      1. Henriksen NM, Gilson M. 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
      2. Shirts MR, Klein C, Swails JM, Yin J, Gilson M, 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 Aug; 31(8):777. PMID: 28752343.
        View in: PubMed
      3. Balius TE, Fischer M, Stein RM, Adler TB, Nguyen CN, Cruz A, Gilson M, Kurtzman T, Shoichet BK. Testing inhomogeneous solvation theory in structure-based ligand discovery. Proc Natl Acad Sci U S A. 2017 Aug 15; 114(33):E6839-E6846. PMID: 28760952.
        View in: PubMed
      4. Heinzelmann G, Henriksen NM, Gilson M. 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
      5. Reany O, Li A, Yefet M, Gilson M, Keinan E. Attractive Interactions between Heteroallenes and the Cucurbituril Portal. J Am Chem Soc. 2017 Jun 21; 139(24):8138-8145. PMID: 28532152.
        View in: PubMed
      6. Chabolla SA, Machan CW, Yin J, Dellamary EA, Sahu S, Gianneschi NC, Gilson M, 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 Jun 02; 198:279-300. PMID: 28374024.
        View in: PubMed
      7. Mobley DL, Gilson M. Predicting Binding Free Energies: Frontiers and Benchmarks. Annu Rev Biophys. 2017 May 22; 46:531-558. PMID: 28399632.
        View in: PubMed
      8. Lee KS, Henriksen NM, Ng CJ, Yang J, Jia W, Morisseau C, Andaya A, Gilson M, 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
      9. Shirts MR, Klein C, Swails JM, Yin J, Gilson M, Mobley DL, Case DA, Zhong ED. Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. J Comput Aided Mol Des. 2017 Jan; 31(1):147-161. PMID: 27787702.
        View in: PubMed
      10. 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 M. 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
      11. Bannan CC, Burley KH, Chiu M, Shirts MR, Gilson M, Mobley DL. Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge. J Comput Aided Mol Des. 2016 Nov; 30(11):927-944. PMID: 27677750.
        View in: PubMed
      12. Yin J, Henriksen NM, Slochower DR, Shirts MR, Chiu MW, Mobley DL, Gilson M. Overview of the SAMPL5 host-guest challenge: Are we doing better? J Comput Aided Mol Des. 2017 Jan; 31(1):1-19. PMID: 27658802.
        View in: PubMed
      13. Yin J, Henriksen NM, Slochower DR, Gilson M. 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 Jan; 31(1):133-145. PMID: 27638809.
        View in: PubMed
      14. Kantonen SA, Henriksen NM, Gilson M. Evaluation and Minimization of Uncertainty in ITC Binding Measurements: Heat Error, Concentration Error, Saturation, and Stoichiometry. Biochim Biophys Acta. 2017 Feb; 1861(2):485-498. PMID: 27599357.
        View in: PubMed
      15. Muddana HS, Sapra NV, Fenley AT, Gilson M. 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
      16. Machan CW, Yin J, Chabolla SA, Gilson M, 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 Jul 06; 138(26):8184-93. PMID: 27258781.
        View in: PubMed
      17. Ramsey S, Nguyen C, Salomon-Ferrer R, Walker RC, Gilson M, Kurtzman T. Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST. J Comput Chem. 2016 Aug 05; 37(21):2029-37. PMID: 27317094.
        View in: PubMed
      18. Li A, Voronin A, Fenley AT, Gilson M. Evaluation of Representations and Response Models for Polarizable Force Fields. J Phys Chem B. 2016 Aug 25; 120(33):8668-84. PMID: 27248842; PMCID: PMC5002935.
      19. Haider K, Wickstrom L, Ramsey S, Gilson M, Kurtzman T. Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces. J Phys Chem B. 2016 Sep 01; 120(34):8743-56. PMID: 27169482; PMCID: PMC5009012 [Available on 09/01/17].
      20. Nguyen CN, Kurtzman T, Gilson M. 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].
      21. Gilson M, 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.
      22. Gao K, Yin J, Henriksen NM, Fenley AT, Gilson M. 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; PMCID: PMC4668924 [Available on 10/13/16].
      23. Nicola G, Berthold MR, Hedrick MP, Gilson M. Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME. Database (Oxford). 2015; 2015. PMID: 26384374; PMCID: PMC4572361.
      24. Henriksen NM, Fenley AT, Gilson M. 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.
      25. Wickstrom L, Deng N, He P, Mentes A, Nguyen C, Gilson M, 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.
      26. Yin J, Fenley AT, Henriksen NM, Gilson M. 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; PMCID: PMC4664157.
      27. Fenley AT, Muddana HS, Gilson M. Calculation and visualization of atomistic mechanical stresses in nanomaterials and biomolecules. PLoS One. 2014; 9(12):e113119. PMID: 25503996; PMCID: PMC4263534.
      28. McClendon CL, Kornev AP, Gilson M, 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.
      29. Blum AP, Kammeyer JK, Yin J, Crystal DT, Rush AM, Gilson M, 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; PMCID: PMC4227725.
      30. Machan CW, Chabolla SA, Yin J, Gilson M, 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
      31. Fenley AT, Henriksen NM, Muddana HS, Gilson M. 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
      32. Fenley AT, Killian BJ, Hnizdo V, Fedorowicz A, Sharp DS, Gilson M. 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.
      33. Nguyen CN, Cruz A, Gilson M, 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
      34. Muddana HS, Fenley AT, Mobley DL, Gilson M. The SAMPL4 host-guest blind prediction challenge: an overview. J Comput Aided Mol Des. 2014 Apr; 28(4):305-17. PMID: 24599514; PMCID: PMC4053502.
      35. Li A, Muddana HS, Gilson M. 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
      36. Gilson M, 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
      37. Muddana HS, Yin J, Sapra NV, Fenley AT, Gilson M. 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.
      38. Muddana HS, Sapra NV, Fenley AT, Gilson M. 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.
      39. Velez-Vega C, Gilson M. 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.
      40. Muddana HS, Sapra NV, Fenley AT, Gilson M. 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.
      41. Fenley AT, Muddana HS, Gilson M. 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.
      42. Orchard S, Binz PA, Borchers C, Gilson M, 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.
      43. Nguyen CN, Young TK, Gilson M. 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.
      44. Nicola G, Liu T, Gilson M. Public domain databases for medicinal chemistry. J Med Chem. 2012 Aug 23; 55(16):6987-7002. PMID: 22731701; PMCID: PMC3427776.
      45. Shen Y, Gilson M, 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
      46. Forrey C, Douglas JF, Gilson M. The Fundamental Role of Flexibility on the Strength of Molecular Binding. Soft Matter. 2012; 8(23):6385-6392. PMID: 22707976.
        View in: PubMed
      47. Muddana HS, Gilson M. 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
      48. Pereira AR, Kale AJ, Fenley AT, Byrum T, Debonsi HM, Gilson M, 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.
      49. Muddana HS, Varnado CD, Bielawski CW, Urbach AR, Isaacs L, Geballe MT, Gilson M. 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.
      50. Muddana HS, Gilson M. 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; PMCID: PMC3383906.
      51. Velez-Vega C, Gilson M. 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
      52. Hecker N, Ahmed J, von Eichborn J, Dunkel M, Macha K, Eckert A, Gilson M, 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.
      53. 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
      54. Somani S, Gilson M. 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.
      55. Moghaddam S, Yang C, Rekharsky M, Ko YH, Kim K, Inoue Y, Gilson M. 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.
      56. Gilson M, 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.
      57. Gilson M, 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.
      58. Chen W, Gilson M, 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
      59. Nalam MN, Ali A, Altman MD, Reddy GS, Chellappan S, Kairys V, Ozen A, Cao H, Gilson M, 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.
      60. Hnizdo V, Gilson M. Thermodynamic and Differential Entropy under a Change of Variables. Entropy (Basel). 2010 Mar 16; 12(3):578-590. PMID: 24436633.
        View in: PubMed
      61. Gilson M. 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
      62. Zhou HX, Gilson M. Theory of free energy and entropy in noncovalent binding. Chem Rev. 2009 Sep; 109(9):4092-107. PMID: 19588959; PMCID: PMC3329805.
      63. Kairys V, Gilson M, 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.
      64. Killian BJ, Kravitz JY, Somani S, Dasgupta P, Pang YP, Gilson M. 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.
      65. Somani S, Killian BJ, Gilson M. Sampling conformations in high dimensions using low-dimensional distribution functions. J Chem Phys. 2009 Apr 07; 130(13):134102. PMID: 19355712; PMCID: PMC2736589.
      66. Moghaddam S, Inoue Y, Gilson M. 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.
      67. Boda D, Valiskó M, Henderson D, Gillespie D, Eisenberg B, Gilson M. 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.
      68. Jorissen RN, Reddy GS, Ali A, Altman MD, Chellappan S, Anjum SG, Tidor B, Schiffer CA, Rana TM, Gilson M. Additivity in the analysis and design of HIV protease inhibitors. J Med Chem. 2009 Feb 12; 52(3):737-54. PMID: 19193159; PMCID: PMC2715819.
      69. Hnizdo V, Tan J, Killian BJ, Gilson M. 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; PMCID: PMC2620139.
      70. Altman MD, Ali A, Reddy GS, Nalam MN, Anjum SG, Cao H, Chellappan S, Kairys V, Fernandes MX, Gilson M, 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; PMCID: PMC3465729.
      71. 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 M, 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.
      72. 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.
      73. 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.
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      74. Chellappan S, Kairys V, Fernandes MX, Schiffer C, Gilson M. 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
      75. Killian BJ, Yundenfreund Kravitz J, Gilson M. Extraction of configurational entropy from molecular simulations via an expansion approximation. J Chem Phys. 2007 Jul 14; 127(2):024107. PMID: 17640119; PMCID: PMC2707031.
      76. 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 M. Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis. Chem Biol Drug Des. 2007 May; 69(5):298-313. PMID: 17539822.
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      77. Chen W, Gilson M. ConCept: de novo design of synthetic receptors for targeted ligands. J Chem Inf Model. 2007 Mar-Apr; 47(2):425-34. PMID: 17315861.
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      78. Chang CE, Chen W, Gilson M. Ligand configurational entropy and protein binding. Proc Natl Acad Sci U S A. 2007 Jan 30; 104(5):1534-9. PMID: 17242351; PMCID: PMC1780070.
      79. Gilson M, Zhou HX. Calculation of protein-ligand binding affinities. Annu Rev Biophys Biomol Struct. 2007; 36:21-42. PMID: 17201676.
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      80. Kairys V, Gilson M, Fernandes MX. Using protein homology models for structure-based studies: approaches to model refinement. ScientificWorldJournal. 2006 Dec 06; 6:1542-54. PMID: 17160340.
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      81. Liu T, Lin Y, Wen X, Jorissen RN, Gilson M. 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.
      82. Chen W, Chang CE, Gilson M. Concepts in receptor optimization: targeting the RGD peptide. J Am Chem Soc. 2006 Apr 12; 128(14):4675-84. PMID: 16594704.
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      83. Gilson M. Sensitivity Analysis and Charge-Optimization for Flexible Ligands:? Applicability to Lead Optimization. J Chem Theory Comput. 2006 Mar; 2(2):259-70. PMID: 26626513.
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      84. Kairys V, Fernandes MX, Gilson M. 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.
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      85. Chang CE, Chen W, Gilson M. Evaluating the Accuracy of the Quasiharmonic Approximation. J Chem Theory Comput. 2005 Sep; 1(5):1017-28. PMID: 26641917.
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      86. Jorissen RN, Gilson M. Virtual screening of molecular databases using a support vector machine. J Chem Inf Model. 2005 May-Jun; 45(3):549-61. PMID: 15921445.
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      87. Fernandes MX, Kairys V, Gilson M. Comparing ligand interactions with multiple receptors via serial docking. J Chem Inf Comput Sci. 2004 Nov-Dec; 44(6):1961-70. PMID: 15554665.
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      88. Chang CE, Gilson M. 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.
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      89. Chen W, Chang CE, Gilson M. Calculation of cyclodextrin binding affinities: energy, entropy, and implications for drug design. Biophys J. 2004 Nov; 87(5):3035-49. PMID: 15339804; PMCID: PMC1304776.
      90. Mihailescu M, Gilson M. On the theory of noncovalent binding. Biophys J. 2004 Jul; 87(1):23-36. PMID: 15240441; PMCID: PMC1304346.
      91. Chen W, Huang J, Gilson M. Identification of symmetries in molecules and complexes. J Chem Inf Comput Sci. 2004 Jul-Aug; 44(4):1301-13. PMID: 15272838.
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      92. Kairys V, Gilson M, 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.
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      93. Chang CE, Gilson M. Tork: Conformational analysis method for molecules and complexes. J Comput Chem. 2003 Dec; 24(16):1987-98. PMID: 14531053.
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      94. Gilson M, 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.
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      95. DeJong ES, Chang CE, Gilson M, 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.
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      96. 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.
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      97. 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.
      98. Kairys V, Gilson M. Enhanced docking with the mining minima optimizer: acceleration and side-chain flexibility. J Comput Chem. 2002 Dec; 23(16):1656-70. PMID: 12395431.
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      99. Luo R, David L, Gilson M. Accelerated Poisson-Boltzmann calculations for static and dynamic systems. J Comput Chem. 2002 Oct; 23(13):1244-53. PMID: 12210150.
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      100. Gilson M. The bioinformatics of molecular recognition. J Mol Recognit. 2002 Jan-Feb; 15(1):1. PMID: 11870915.
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      101. Chen X, Lin Y, Liu M, Gilson M. The Binding Database: data management and interface design. Bioinformatics. 2002 Jan; 18(1):130-9. PMID: 11836221.
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      102. Chen X, Liu M, Gilson M. BindingDB: a web-accessible molecular recognition database. Comb Chem High Throughput Screen. 2001 Dec; 4(8):719-25. PMID: 11812264.
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      103. Mardis KL, Luo R, Gilson M. Interpreting trends in the binding of cyclic ureas to HIV-1 protease. J Mol Biol. 2001 Jun 01; 309(2):507-17. PMID: 11371168.
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      104. David L, Luo R, Gilson M. Ligand-receptor docking with the Mining Minima optimizer. J Comput Aided Mol Des. 2001 Feb; 15(2):157-71. PMID: 11272702.
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      105. Luo R, Gilson HS, Potter MJ, Gilson M. The physical basis of nucleic acid base stacking in water. Biophys J. 2001 Jan; 80(1):140-8. PMID: 11159389; PMCID: PMC1301220.
      106. Chen X, Lin Y, Gilson M. The binding database: overview and user's guide. Biopolymers. 2001-2002; 61(2):127-41. PMID: 11987162.
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      107. Mardis K, Luo R, David L, Potter M, Glemza A, Payne G, Gilson M. Modeling molecular recognition: theory and application. J Biomol Struct Dyn. 2000; 17 Suppl 1:89-94. PMID: 22607411.
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      108. Luo R, Head MS, Given JA, Gilson M. 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.
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      109. Trylska J, Antosiewicz J, Geller M, Hodge CN, Klabe RM, Head MS, Gilson M. Thermodynamic linkage between the binding of protons and inhibitors to HIV-1 protease. Protein Sci. 1999 Jan; 8(1):180-95. PMID: 10210196; PMCID: PMC2144115.
      110. Given JA, Gilson M. A hierarchical method for generating low-energy conformers of a protein-ligand complex. Proteins. 1998 Dec 01; 33(4):475-95. PMID: 9849934.
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      111. Forsyth WR, Gilson M, 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.
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      112. 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.
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      113. Gilson M, 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; PMCID: PMC1184492.
      114. Gilson M, 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.
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      115. Antosiewicz J, McCammon JA, Gilson M. The determinants of pKas in proteins. Biochemistry. 1996 Jun 18; 35(24):7819-33. PMID: 8672483.
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      116. Wlodek ST, Antosiewicz J, McCammon JA, Straatsma TP, Gilson M, Briggs JM, Humblet C, Sussman JL. Binding of tacrine and 6-chlorotacrine by acetylcholinesterase. Biopolymers. 1996 Jan; 38(1):109-17. PMID: 8679940.
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      117. Antosiewicz J, McCammon JA, Wlodek ST, Gilson M. Simulation of charge-mutant acetylcholinesterases. Biochemistry. 1995 Apr 04; 34(13):4211-9. PMID: 7703233.
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      118. Gilson M. Theory of electrostatic interactions in macromolecules. Curr Opin Struct Biol. 1995 Apr; 5(2):216-23. PMID: 7648324.
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      119. Antosiewicz J, Gilson M, Lee IH, McCammon JA. Acetylcholinesterase: diffusional encounter rate constants for dumbbell models of ligand. Biophys J. 1995 Jan; 68(1):62-8. PMID: 7711269; PMCID: PMC1281661.
      120. Antosiewicz J, McCammon JA, Gilson M. Prediction of pH-dependent properties of proteins. J Mol Biol. 1994 May 06; 238(3):415-36. PMID: 8176733.
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      121. Gilson M, 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.
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      122. Gilson M. 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.
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      123. Gilson M, 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.
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      124. Gilson M, 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; PMCID: PMC286730.
      125. Honig B, Sharp K, Gilson M. Electrostatic interactions in proteins. Prog Clin Biol Res. 1989; 289:65-74. PMID: 2726810.
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      126. Roy H, Cannon S, Gilson M. Assembly of Rubisco from native subunits. Biochim Biophys Acta. 1988 Dec 02; 957(3):323-34. PMID: 3058207.
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      127. Gilson M, 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.
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      128. Gilson M, Honig BH. Energetics of charge-charge interactions in proteins. Proteins. 1988; 3(1):32-52. PMID: 3287370.
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      129. Gilson M, Honig BH. Calculation of electrostatic potentials in an enzyme active site. Nature. 1987 Nov 5-11; 330(6143):84-6. PMID: 3313058.
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      130. Gilson M, Honig BH. The dielectric constant of a folded protein. Biopolymers. 1986 Nov; 25(11):2097-119. PMID: 3790703.
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      131. Gilson M, 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.
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