Michael K Gilson

Title(s)Professor and Chair in Computer-Aided Drug Design, School of Pharmacy and Pharmaceutical Science
SchoolHealth Sciences
Address9500 Gilman Drive #0736
La Jolla CA 92093
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    Collapse Research Activities and Funding
    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
    Computational Anatomy and Multidimensional Modeling
    NIH P41RR013642Sep 7, 2009 - Sep 6, 2012
    Role: Co-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 - Dec 31, 2009
    Role: Principal Investigator
    Inexpensive Interactive Molecular Modeling Software
    NIH R42GM062050Jul 20, 2000 - Apr 30, 2006
    Role: Principal Investigator
    NIH R41GM062050Jul 20, 2000 - Jan 19, 2002
    Role: Principal Investigator
    NIH R29GM054053May 1, 1996 - Aug 31, 2000
    Role: Principal Investigator

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    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. 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. Automation of absolute protein-ligand binding free energy calculations for docking refinement and compound evaluation. Sci Rep. 2021 Jan 13; 11(1):1116. Heinzelmann G, Gilson MK. PMID: 33441879.
      View in: PubMed   Mentions:    Fields:    
    2. Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations. J Chem Theory Comput. 2020 Nov 18. Ben-Shalom IY, Lin Z, Radak BK, Lin C, Sherman W, Gilson MK. PMID: 33206520.
      View in: PubMed   Mentions: 1     Fields:    
    3. Experimental characterization of the association of ß-cyclodextrin and eight novel cyclodextrin derivatives with two guest compounds. J Comput Aided Mol Des. 2021 Jan; 35(1):95-104. PMID: 33037548.
      View in: PubMed   Mentions:    Fields:    
    4. Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo. J Comput Aided Mol Des. 2020 Sep 24. Bergazin TD, Ben-Shalom IY, Lim NM, Gill SC, Gilson MK, Mobley DL. PMID: 32968887.
      View in: PubMed   Mentions:    Fields:    
    5. 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:    
    6. 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: 1     Fields:    Translation:Cells
    7. 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.
      View in: PubMed   Mentions: 3     Fields:    
    8. 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.
      View in: PubMed   Mentions: 3     Fields:    
    9. 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.
      View in: PubMed   Mentions:    Fields:    
    10. 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
    11. 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.
      View in: PubMed   Mentions: 2     Fields:    
    12. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    13. 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.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    14. 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.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    15. 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.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    16. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    17. 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.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    18. 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.
      View in: PubMed   Mentions: 28     Fields:    Translation:Cells
    19. 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.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    20. 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.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    21. 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.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    22. 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.
      View in: PubMed   Mentions: 7     Fields:    
    23. 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.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    24. 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.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    25. 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.
      View in: PubMed   Mentions: 2     Fields:    
    26. Motor-like Properties of Nonmotor Enzymes. Biophys J. 2018 05 08; 114(9):2174-2179. Slochower DR, Gilson MK. PMID: 29742410.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    27. Substrate-driven chemotactic assembly in an enzyme cascade. Nat Chem. 2018 03; 10(3):311-317. PMID: 29461522.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    28. 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.
      View in: PubMed   Mentions: 4     Fields:    
    29. 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.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    30. 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   Mentions: 40     Fields:    Translation:HumansCells
    31. 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.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    32. 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   Mentions: 7     Fields:    
    33. 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:    
    34. 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.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    35. 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   Mentions: 11     Fields:    Translation:HumansCells
    36. Attractive Interactions between Heteroallenes and the Cucurbituril Portal. J Am Chem Soc. 2017 06 21; 139(24):8138-8145. PMID: 28532152.
      View in: PubMed   Mentions:    Fields:    
    37. 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.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    38. Predicting Binding Free Energies: Frontiers and Benchmarks. Annu Rev Biophys. 2017 05 22; 46:531-558. PMID: 28399632.
      View in: PubMed   Mentions: 33     Fields:    Translation:Cells
    39. 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   Mentions:    Fields:    Translation:HumansCells
    40. 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   Mentions: 8     Fields:    Translation:Cells
    41. 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   Mentions: 60     Fields:    Translation:Cells
    42. 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   Mentions: 35     Fields:    Translation:Cells
    43. 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   Mentions: 38     Fields:    Translation:Cells
    44. 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   Mentions: 12     Fields:    Translation:Cells
    45. 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   Mentions: 3     Fields:    Translation:Cells
    46. Erratum: "The electrostatic response of water to neutral polar solutes: Implications for continuum solvent modeling" [J. Chem. Phys. 138, 224504 (2013)]. J Chem Phys. 2016 07 28; 145(4):049902. PMID: 27475401.
      View in: PubMed   Mentions:    Fields:    
    47. 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   Mentions: 4     Fields:    Translation:Cells
    48. Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST. J Comput Chem. 2016 08 05; 37(21):2029-37. PMID: 27317094.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    49. 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   Mentions: 2     Fields:    
    50. 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   Mentions: 5     Fields:    Translation:Cells
    51. Spatial Decomposition of Translational Water-Water Correlation Entropy in Binding Pockets. J Chem Theory Comput. 2016 Jan 12; 12(1):414-29. PMID: 26636620.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    52. 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.
      View in: PubMed   Mentions: 122     Fields:    Translation:Cells
    53. 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   Mentions: 5     Fields:    Translation:Cells
    54. Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME. Database (Oxford). 2015; 2015. PMID: 26384374.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    55. Computational Calorimetry: High-Precision Calculation of Host-Guest Binding Thermodynamics. J Chem Theory Comput. 2015 Sep 08; 11(9):4377-94. PMID: 26523125.
      View in: PubMed   Mentions: 24     Fields:    Translation:Cells
    56. 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.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    57. 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   Mentions: 8     Fields:    Translation:Cells
    58. Calculation and visualization of atomistic mechanical stresses in nanomaterials and biomolecules. PLoS One. 2014; 9(12):e113119. PMID: 25503996.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    59. Dynamic architecture of a protein kinase. Proc Natl Acad Sci U S A. 2014 Oct 28; 111(43):E4623-31. PMID: 25319261.
      View in: PubMed   Mentions: 57     Fields:    Translation:Cells
    60. 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   Mentions: 12     Fields:    Translation:HumansCells
    61. 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   Mentions: 10     Fields:    Translation:Cells
    62. 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   Mentions: 20     Fields:    
    63. 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.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    64. 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   Mentions: 33     Fields:    
    65. The SAMPL4 host-guest blind prediction challenge: an overview. J Comput Aided Mol Des. 2014 Apr; 28(4):305-17. PMID: 24599514.
      View in: PubMed   Mentions: 60     Fields:    Translation:Cells
    66. 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   Mentions: 9     Fields:    
    67. Digital chemistry in the Journal of Medicinal Chemistry. J Med Chem. 2014 Feb 27; 57(4):1137. PMID: 24521446.
      View in: PubMed   Mentions: 7     Fields:    
    68. 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.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    69. 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.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    70. 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.
      View in: PubMed   Mentions: 25     Fields:    Translation:Cells
    71. 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.
      View in: PubMed   Mentions: 8     Fields:    
    72. 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.
      View in: PubMed   Mentions: 35     Fields:    Translation:AnimalsCells
    73. 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.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    74. 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.
      View in: PubMed   Mentions: 74     Fields:    Translation:Cells
    75. Public domain databases for medicinal chemistry. J Med Chem. 2012 Aug 23; 55(16):6987-7002. PMID: 22731701.
      View in: PubMed   Mentions: 14     Fields:    
    76. Charge Optimization Theory for Induced-Fit Ligands. J Chem Theory Comput. 2012 Nov 13; 8(11):4580-4592. PMID: 23162383.
      View in: PubMed   Mentions: 1     Fields:    
    77. The Fundamental Role of Flexibility on the Strength of Molecular Binding. Soft Matter. 2012; 8(23):6385-6392. PMID: 22707976.
      View in: PubMed   Mentions: 11     Fields:    
    78. 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   Mentions: 21     Fields:    
    79. 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.
      View in: PubMed   Mentions: 24     Fields:    Translation:AnimalsCells
    80. Blind prediction of host-guest binding affinities: a new SAMPL3 challenge. J Comput Aided Mol Des. 2012 May; 26(5):475-87. PMID: 22366955.
      View in: PubMed   Mentions: 53     Fields:    Translation:HumansCells
    81. 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   Mentions: 16     Fields:    Translation:Cells
    82. 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   Mentions: 6     Fields:    
    83. SuperTarget goes quantitative: update on drug-target interactions. Nucleic Acids Res. 2012 Jan; 40(Database issue):D1113-7. PMID: 22067455.
      View in: PubMed   Mentions: 45     Fields:    Translation:Cells
    84. Minimum information about a bioactive entity (MIABE). Nat Rev Drug Discov. 2011 Aug 31; 10(9):661-9. 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. PMID: 21878981.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansAnimals
    85. Accelerated convergence of molecular free energy via superposition approximation-based reference states. J Chem Phys. 2011 Apr 07; 134(13):134107. Somani S, Gilson MK. PMID: 21476743.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    86. New ultrahigh affinity host-guest complexes of cucurbit[7]uril with bicyclo[2.2.2]octane and adamantane guests: thermodynamic analysis and evaluation of M2 affinity calculations. J Am Chem Soc. 2011 Mar 16; 133(10):3570-81. Moghaddam S, Yang C, Rekharsky M, Ko YH, Kim K, Inoue Y, Gilson MK. PMID: 21341773.
      View in: PubMed   Mentions: 57     Fields:    
    87. Protein folding and binding: from biology to physics and back again. Curr Opin Struct Biol. 2011 Feb; 21(1):1-3. PMID: 21196111.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    88. Symmetry numbers for rigid, flexible, and fluxional molecules: theory and applications. J Phys Chem B. 2010 Dec 16; 114(49):16304-17. Gilson MK, Irikura KK. PMID: 21141931.
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    89. Modeling Protein-Ligand Binding by Mining Minima. J Chem Theory Comput. 2010 Nov 09; 6(11):3540-3557. PMID: 22639555.
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    90. Evaluating the substrate-envelope hypothesis: structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance. J Virol. 2010 May; 84(10):5368-78. Nalam MN, Ali A, Altman MD, Reddy GS, Chellappan S, Kairys V, Ozen A, Cao H, Gilson MK, Tidor B, Rana TM, Schiffer CA. PMID: 20237088.
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    91. Thermodynamic and Differential Entropy under a Change of Variables. Entropy (Basel). 2010 Mar 16; 12(3):578-590. PMID: 24436633.
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    92. 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.
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    93. Theory of free energy and entropy in noncovalent binding. Chem Rev. 2009 Sep; 109(9):4092-107. Zhou HX, Gilson MK. PMID: 19588959.
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    94. Toward the design of mutation-resistant enzyme inhibitors: further evaluation of the substrate envelope hypothesis. Chem Biol Drug Des. 2009 Sep; 74(3):234-45. Kairys V, Gilson MK, Lather V, Schiffer CA, Fernandes MX. PMID: 19703025.
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    95. Configurational entropy in protein-peptide binding: computational study of Tsg101 ubiquitin E2 variant domain with an HIV-derived PTAP nonapeptide. J Mol Biol. 2009 Jun 05; 389(2):315-35. Killian BJ, Kravitz JY, Somani S, Dasgupta P, Pang YP, Gilson MK. PMID: 19362095.
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    96. Sampling conformations in high dimensions using low-dimensional distribution functions. J Chem Phys. 2009 Apr 07; 130(13):134102. Somani S, Killian BJ, Gilson MK. PMID: 19355712.
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    97. Host-guest complexes with protein-ligand-like affinities: computational analysis and design. J Am Chem Soc. 2009 Mar 25; 131(11):4012-21. Moghaddam S, Inoue Y, Gilson MK. PMID: 19133781.
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    98. Ions and inhibitors in the binding site of HIV protease: comparison of Monte Carlo simulations and the linearized Poisson-Boltzmann theory. Biophys J. 2009 Feb 18; 96(4):1293-306. Boda D, Valiskó M, Henderson D, Gillespie D, Eisenberg B, Gilson MK. PMID: 19217848.
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    99. Additivity in the analysis and design of HIV protease inhibitors. J Med Chem. 2009 Feb 12; 52(3):737-54. Jorissen RN, Reddy GS, Ali A, Altman MD, Chellappan S, Anjum SG, Tidor B, Schiffer CA, Rana TM, Gilson MK. PMID: 19193159.
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    100. Efficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methods. J Comput Chem. 2008 Jul 30; 29(10):1605-14. Hnizdo V, Tan J, Killian BJ, Gilson MK. PMID: 18293293.
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    101. HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants. J Am Chem Soc. 2008 May 14; 130(19):6099-113. Altman MD, Ali A, Reddy GS, Nalam MN, Anjum SG, Cao H, Chellappan S, Kairys V, Fernandes MX, Gilson MK, Schiffer CA, Rana TM, Tidor B. PMID: 18412349.
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    102. A synthetic host-guest system achieves avidin-biotin affinity by overcoming enthalpy-entropy compensation. Proc Natl Acad Sci U S A. 2007 Dec 26; 104(52):20737-42. Rekharsky MV, Mori T, Yang C, Ko YH, Selvapalam N, Kim H, Sobransingh D, Kaifer AE, Liu S, Isaacs L, Chen W, Moghaddam S, Gilson MK, Kim K, Inoue Y. PMID: 18093926.
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    103. Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol. 2007 Oct 09; 5:44. Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stümpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H. PMID: 17925023.
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    104. Evaluation of the substrate envelope hypothesis for inhibitors of HIV-1 protease. Proteins. 2007 Aug 01; 68(2):561-7. Chellappan S, Kairys V, Fernandes MX, Schiffer C, Gilson MK. PMID: 17474129.
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    105. The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol. 2007 Aug; 25(8):894-8. Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stümpflen V, Ceol A, Chatr-aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, De Las Rivas J, Prieto C, Perreau VM, Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H. PMID: 17687370.
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    106. Extraction of configurational entropy from molecular simulations via an expansion approximation. J Chem Phys. 2007 Jul 14; 127(2):024107. Killian BJ, Yundenfreund Kravitz J, Gilson MK. PMID: 17640119.
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    107. Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis. Chem Biol Drug Des. 2007 May; 69(5):298-313. Chellappan S, Kiran Kumar Reddy GS, Ali A, Nalam MN, Anjum SG, Cao H, Kairys V, Fernandes MX, Altman MD, Tidor B, Rana TM, Schiffer CA, Gilson MK. PMID: 17539822.
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    108. ConCept: de novo design of synthetic receptors for targeted ligands. J Chem Inf Model. 2007 Mar-Apr; 47(2):425-34. Chen W, Gilson MK. PMID: 17315861.
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    109. Ligand configurational entropy and protein binding. Proc Natl Acad Sci U S A. 2007 Jan 30; 104(5):1534-9. Chang CE, Chen W, Gilson MK. PMID: 17242351.
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    110. Calculation of protein-ligand binding affinities. Annu Rev Biophys Biomol Struct. 2007; 36:21-42. Gilson MK, Zhou HX. PMID: 17201676.
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    111. Using protein homology models for structure-based studies: approaches to model refinement. ScientificWorldJournal. 2006 Dec 06; 6:1542-54. Kairys V, Gilson MK, Fernandes MX. PMID: 17160340.
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    112. 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.
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    113. 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.
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    114. 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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    115. 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.
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    116. Evaluating the Accuracy of the Quasiharmonic Approximation. J Chem Theory Comput. 2005 Sep; 1(5):1017-28. PMID: 26641917.
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    117. 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.
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    118. 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.
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    119. 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.
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    120. 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.
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    121. On the theory of noncovalent binding. Biophys J. 2004 Jul; 87(1):23-36. Mihailescu M, Gilson MK. PMID: 15240441.
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    122. 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.
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    123. 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: 7     Fields:    Translation:HumansAnimalsCells
    124. Tork: Conformational analysis method for molecules and complexes. J Comput Chem. 2003 Dec; 24(16):1987-98. Chang CE, Gilson MK. PMID: 14531053.
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    125. 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.
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    126. 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: 19     Fields:    Translation:HumansCells
    127. 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.
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    128. 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.
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    129. 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.
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    130. Accelerated Poisson-Boltzmann calculations for static and dynamic systems. J Comput Chem. 2002 Oct; 23(13):1244-53. Luo R, David L, Gilson MK. PMID: 12210150.
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    131. 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.
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    132. The bioinformatics of molecular recognition. J Mol Recognit. 2002 Jan-Feb; 15(1):1. Gilson MK. PMID: 11870915.
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    133. 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.
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    134. 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.
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    135. 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.
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    136. The binding database: overview and user's guide. Biopolymers. 2001-2002; 61(2):127-41. Chen X, Lin Y, Gilson MK. PMID: 11987162.
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    137. 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.
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    138. Modeling molecular recognition: theory and application. J Biomol Struct Dyn. 2000; 17 Suppl 1:89-94. PMID: 22607411.
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    139. 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.
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    140. 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.
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    141. 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.
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    142. 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.
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    143. 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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    144. 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.
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    145. 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.
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    146. The determinants of pKas in proteins. Biochemistry. 1996 Jun 18; 35(24):7819-33. Antosiewicz J, McCammon JA, Gilson MK. PMID: 8672483.
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    147. Binding of tacrine and 6-chlorotacrine by acetylcholinesterase. Biopolymers. 1996 Jan; 38(1):109-17. Wlodek ST, Antosiewicz J, McCammon JA, Straatsma TP, Gilson MK, Briggs JM, Humblet C, Sussman JL. PMID: 8679940.
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    148. Simulation of charge-mutant acetylcholinesterases. Biochemistry. 1995 Apr 04; 34(13):4211-9. Antosiewicz J, McCammon JA, Wlodek ST, Gilson MK. PMID: 7703233.
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    149. Theory of electrostatic interactions in macromolecules. Curr Opin Struct Biol. 1995 Apr; 5(2):216-23. Gilson MK. PMID: 7648324.
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    150. 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.
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    151. Prediction of pH-dependent properties of proteins. J Mol Biol. 1994 May 06; 238(3):415-36. Antosiewicz J, McCammon JA, Gilson MK. PMID: 8176733.
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    152. Open "back door" in a molecular dynamics simulation of acetylcholinesterase. Science. 1994 Mar 04; 263(5151):1276-8. Gilson MK, Straatsma TP, McCammon JA, Ripoll DR, Faerman CH, Axelsen PH, Silman I, Sussman JL. PMID: 8122110.
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    153. 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.
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    154. 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.
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    155. 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.
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    156. Electrostatic interactions in proteins. Prog Clin Biol Res. 1989; 289:65-74. Honig B, Sharp K, Gilson M. PMID: 2726810.
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    157. Energetics of charge-charge interactions in proteins. Proteins. 1988; 3(1):32-52. Gilson MK, Honig BH. PMID: 3287370.
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    158. 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.
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    159. Calculation of electrostatic potentials in an enzyme active site. Nature. 1987 Nov 5-11; 330(6143):84-6. Gilson MK, Honig BH. PMID: 3313058.
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    160. The dielectric constant of a folded protein. Biopolymers. 1986 Nov; 25(11):2097-119. Gilson MK, Honig BH. PMID: 3790703.
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    161. 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.
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