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J. Andrew Mccammon

TitleProfessor
InstitutionUniversity of California San Diego
DepartmentPharmacology
Address9500 Gilman Drive #0365
La Jolla CA 92093
Phone858-534-2905
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    Collapse Biography 
    Collapse Education and Training
    Harvard UniversityPh.D.1976Chemical Physics
    Pomona CollegeB.A.1969Chemistry, Mathematics and Physics
    Collapse Awards and Honors
    Ohio State University2017Russell M. Pitzer Award and Lecture in Theoretical Chemistry
    University of Wisconsin2016  - 2017Hirschfelder Prize in Theoretical Chemistry
    US National Academy of Sciences2011Member
    American Chemical Society2008National Award for Computers in Chemical and Pharmaceutical Research
    American Academy of Arts and Sciences2006Fellow
    Howard Hughes Medical Institute2000Investigator
    Smithsonian Institution1995Award for Breakthrough Computational Science
    Burroughs Wellcome Fund1987  - 1992G.H. Hitchings Award for Innovative Methods in Drug Design
    1982  - 1987Camille and Henry Dreyfus Teacher–Scholar Award
    1980  - 1985NIH Research Career Development Award
    1980  - 1984Alfred P. Sloan Research Fellow

    Collapse Overview 

    Collapse Research 
    Collapse Research Activities and Funding
    Protein-Protein Interaction in Natural Product Biosynthesis
    NIH/NIGMS R01GM095970Mar 1, 2012 - Jan 31, 2020
    Role: Principal Investigator
    Theory of Biomolecular Diffusion
    NIH R01GM031749Jun 1, 1983 - Jun 30, 2019
    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. Miao Y, McCammon JA. Mechanism of the G-protein mimetic nanobody binding to a muscarinic G-protein-coupled receptor. Proc Natl Acad Sci U S A. 2018 Mar 20; 115(12):3036-3041. PMID: 29507218.
      View in: PubMed
    2. Palermo G, Ricci CG, Fernando A, Basak R, Jinek M, Rivalta I, Batista VS, McCammon JA. Protospacer Adjacent Motif-Induced Allostery Activates CRISPR-Cas9. J Am Chem Soc. 2017 Nov 15; 139(45):16028-16031. PMID: 28764328.
      View in: PubMed
    3. Caliman AD, Miao Y, McCammon JA. Mapping the allosteric sites of the A2A adenosine receptor. Chem Biol Drug Des. 2018 Jan; 91(1):5-16. PMID: 28639411.
      View in: PubMed
    4. Ricci CG, Li B, Cheng LT, Dzubiella J, McCammon JA. "Martinizing" the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins. J Phys Chem B. 2017 07 13; 121(27):6538-6548. PMID: 28613904.
      View in: PubMed
    5. Palermo G, Miao Y, Walker RC, Jinek M, McCammon JA. CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations. Proc Natl Acad Sci U S A. 2017 07 11; 114(28):7260-7265. PMID: 28652374.
      View in: PubMed
    6. Caliman AD, Miao Y, McCammon JA. Activation mechanisms of the first sphingosine-1-phosphate receptor. Protein Sci. 2017 Jun; 26(6):1150-1160. PMID: 28370663.
      View in: PubMed
    7. Dick BL, Patel A, McCammon JA, Cohen SM. Effect of donor atom identity on metal-binding pharmacophore coordination. J Biol Inorg Chem. 2017 Jun; 22(4):605-613. PMID: 28389830.
      View in: PubMed
    8. O'Dowd B, Williams S, Wang H, No JH, Rao G, Wang W, McCammon JA, Cramer SP, Oldfield E. Spectroscopic and Computational Investigations of Ligand Binding to IspH: Discovery of Non-diphosphate Inhibitors. Chembiochem. 2017 05 18; 18(10):914-920. PMID: 28253432.
      View in: PubMed
    9. Chan AH, Yi SW, Weiner EM, Amer BR, Sue CK, Wereszczynski J, Dillen CA, Senese S, Torres JZ, McCammon JA, Miller LS, Jung ME, Clubb RT. NMR structure-based optimization of Staphylococcus aureus sortase A pyridazinone inhibitors. Chem Biol Drug Des. 2017 Sep; 90(3):327-344. PMID: 28160417.
      View in: PubMed
    10. Pang YT, Miao Y, Wang Y, McCammon JA. Gaussian Accelerated Molecular Dynamics in NAMD. J Chem Theory Comput. 2017 01 10; 13(1):9-19. PMID: 28034310.
      View in: PubMed
    11. Miao Y, McCammon JA. Graded activation and free energy landscapes of a muscarinic G-protein-coupled receptor. Proc Natl Acad Sci U S A. 2016 10 25; 113(43):12162-12167. PMID: 27791003.
      View in: PubMed
    12. Palermo G, Miao Y, Walker RC, Jinek M, McCammon JA. Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations. ACS Cent Sci. 2016 Oct 26; 2(10):756-763. PMID: 27800559.
      View in: PubMed
    13. Miao Y, Goldfeld DA, Moo EV, Sexton PM, Christopoulos A, McCammon JA, Valant C. Accelerated structure-based design of chemically diverse allosteric modulators of a muscarinic G protein-coupled receptor. Proc Natl Acad Sci U S A. 2016 09 20; 113(38):E5675-84. PMID: 27601651.
      View in: PubMed
    14. G Ricci C, Liu YL, Zhang Y, Wang Y, Zhu W, Oldfield E, McCammon JA. Dynamic Structure and Inhibition of a Malaria Drug Target: Geranylgeranyl Diphosphate Synthase. Biochemistry. 2016 09 13; 55(36):5180-90. PMID: 27564465.
      View in: PubMed
    15. McCammon JA. Autobiography of J. Andrew McCammon. J Phys Chem B. 2016 08 25; 120(33):8057-60. PMID: 27558539.
      View in: PubMed
    16. Zhou S, Sun H, Cheng LT, Dzubiella J, Li B, McCammon JA. Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations. J Chem Phys. 2016 Aug 07; 145(5):054114. PMID: 27497546; PMCID: PMC4975753 [Available on 08/07/17].
    17. Miao Y, McCammon JA. Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review. Mol Simul. 2016; 42(13):1046-1055. PMID: 27453631.
      View in: PubMed
    18. Miao Y, McCammon JA. G-protein coupled receptors: advances in simulation and drug discovery. Curr Opin Struct Biol. 2016 12; 41:83-89. PMID: 27344006.
      View in: PubMed
    19. Huang YM, Miao Y, Munguia J, Lin L, Nizet V, McCammon JA. Molecular dynamic study of MlaC protein in Gram-negative bacteria: conformational flexibility, solvent effect and protein-phospholipid binding. Protein Sci. 2016 08; 25(8):1430-7. PMID: 27111825; PMCID: PMC4972199 [Available on 08/01/17].
    20. Mouchlis VD, Morisseau C, Hammock BD, Li S, McCammon JA, Dennis EA. Computer-aided drug design guided by hydrogen/deuterium exchange mass spectrometry: A powerful combination for the development of potent and selective inhibitors of Group VIA calcium-independent phospholipase A2. Bioorg Med Chem. 2016 10 15; 24(20):4801-4811. PMID: 27320659.
      View in: PubMed
    21. Huber GA, Miao Y, Zhou S, Li B, McCammon JA. Hybrid finite element and Brownian dynamics method for charged particles. J Chem Phys. 2016 Apr 28; 144(16):164107. PMID: 27131531; PMCID: PMC4851620 [Available on 04/28/17].
    22. Mouchlis VD, Limnios D, Kokotou MG, Barbayianni E, Kokotos G, McCammon JA, Dennis EA. Development of Potent and Selective Inhibitors for Group VIA Calcium-Independent Phospholipase A2 Guided by Molecular Dynamics and Structure-Activity Relationships. J Med Chem. 2016 05 12; 59(9):4403-14. PMID: 27087127; PMCID: PMC4946799 [Available on 05/12/17].
    23. Miao Y, Baudry J, Smith JC, McCammon JA. General trends of dihedral conformational transitions in a globular protein. Proteins. 2016 Apr; 84(4):501-14. PMID: 26799251.
      View in: PubMed
    24. Kim MO, McCammon JA. Computation of pH-dependent binding free energies. Biopolymers. 2016 Jan; 105(1):43-9. PMID: 26202905; PMCID: PMC4623928 [Available on 01/01/17].
    25. Sun H, Wen J, Zhao Y, Li B, McCammon JA. A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson-Boltzmann electrostatics. J Chem Phys. 2015 Dec 28; 143(24):243110. PMID: 26723595; PMCID: PMC4605633 [Available on 12/28/16].
    26. Feng X, Zhu W, Schurig-Briccio LA, Lindert S, Shoen C, Hitchings R, Li J, Wang Y, Baig N, Zhou T, Kim BK, Crick DC, Cynamon M, McCammon JA, Gennis RB, Oldfield E. Antiinfectives targeting enzymes and the proton motive force. Proc Natl Acad Sci U S A. 2015 Dec 22; 112(51):E7073-82. PMID: 26644565; PMCID: PMC4697371.
    27. Kappel K, Miao Y, McCammon JA. Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor. Q Rev Biophys. 2015 Nov; 48(4):479-87. PMID: 26537408.
      View in: PubMed
    28. Kim MO, Blachly PG, McCammon JA. Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria. PLoS Comput Biol. 2015 Oct; 11(10):e1004341. PMID: 26506513; PMCID: PMC4623973.
    29. Cheng Y, Rao V, Tu AY, Lindert S, Wang D, Oxenford L, McCulloch AD, McCammon JA, Regnier M. Troponin I Mutations R146G and R21C Alter Cardiac Troponin Function, Contractile Properties, and Modulation by Protein Kinase A (PKA)-mediated Phosphorylation. J Biol Chem. 2015 Nov 13; 290(46):27749-66. PMID: 26391394; PMCID: PMC4646022 [Available on 11/13/16].
    30. Huang YM, Huber G, McCammon JA. Electrostatic steering enhances the rate of cAMP binding to phosphodiesterase: Brownian dynamics modeling. Protein Sci. 2015 Nov; 24(11):1884-9. PMID: 26346301; PMCID: PMC4622220 [Available on 11/01/16].
    31. Kekenes-Huskey PM, Eun C, McCammon JA. Enzyme localization, crowding, and buffers collectively modulate diffusion-influenced signal transduction: Insights from continuum diffusion modeling. J Chem Phys. 2015 Sep 07; 143(9):094103. PMID: 26342355; PMCID: PMC4560719.
    32. Miao Y, Feher VA, McCammon JA. Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation. J Chem Theory Comput. 2015 Aug 11; 11(8):3584-3595. PMID: 26300708.
      View in: PubMed
    33. Wang N, McCammon JA. Substrate channeling between the human dihydrofolate reductase and thymidylate synthase. Protein Sci. 2016 Jan; 25(1):79-86. PMID: 26096018; PMCID: PMC4815301 [Available on 01/01/17].
    34. Blachly PG, Sandala GM, Giammona DA, Bashford D, McCammon JA, Noodleman L. Broken-Symmetry DFT Computations for the Reaction Pathway of IspH, an Iron-Sulfur Enzyme in Pathogenic Bacteria. Inorg Chem. 2015 Jul 06; 54(13):6439-61. PMID: 26098647; PMCID: PMC4568833.
    35. Miao Y, Feixas F, Eun C, McCammon JA. Accelerated molecular dynamics simulations of protein folding. J Comput Chem. 2015 Jul 30; 36(20):1536-49. PMID: 26096263; PMCID: PMC4487363.
    36. Kaus JW, Harder E, Lin T, Abel R, McCammon JA, Wang L. How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations. J Chem Theory Comput. 2015 Jun 09; 11(6):2670-9. PMID: 26085821; PMCID: PMC4462751.
    37. Kaus JW, McCammon JA. Enhanced ligand sampling for relative protein-ligand binding free energy calculations. J Phys Chem B. 2015 May 21; 119(20):6190-7. PMID: 25906170; PMCID: PMC4442669.
    38. Caliman AD, Swift SE, Wang Y, Miao Y, McCammon JA. Investigation of the conformational dynamics of the apo A2A adenosine receptor. Protein Sci. 2015 Jun; 24(6):1004-12. PMID: 25761901; PMCID: PMC4456113.
    39. Miao Y, Caliman AD, McCammon JA. Allosteric effects of sodium ion binding on activation of the m3 muscarinic g-protein-coupled receptor. Biophys J. 2015 Apr 07; 108(7):1796-1806. PMID: 25863070.
      View in: PubMed
    40. Kekenes-Huskey PM, Gillette AK, McCammon JA. Erratum: "Predicting the influence of long-range molecular interactions on macroscopic-scale diffusion by homogenization of the Smoluchowski equation" [J. Chem. Phys. 140, 174106 (2014)]. J Chem Phys. 2015 Mar 14; 142(10):109902. PMID: 25770569.
      View in: PubMed
    41. Zhou S, Cheng LT, Sun H, Che J, Dzubiella J, Li B, McCammon JA. LS-VISM: A software package for analysis of biomolecular solvation. J Comput Chem. 2015 May 30; 36(14):1047-59. PMID: 25766844; PMCID: PMC4412808.
    42. Lindert S, McCammon JA. Improved cryoEM-Guided Iterative Molecular Dynamics--Rosetta Protein Structure Refinement Protocol for High Precision Protein Structure Prediction. J Chem Theory Comput. 2015 Mar 10; 11(3):1337-46. PMID: 25883538; PMCID: PMC4393324.
    43. Guo Z, Li B, Cheng LT, Zhou S, McCammon JA, Che J. Identification of protein-ligand binding sites by the level-set variational implicit-solvent approach. J Chem Theory Comput. 2015 Feb 10; 11(2):753-65. PMID: 25941465; PMCID: PMC4410907.
    44. Mouchlis VD, Bucher D, McCammon JA, Dennis EA. Membranes serve as allosteric activators of phospholipase A2, enabling it to extract, bind, and hydrolyze phospholipid substrates. Proc Natl Acad Sci U S A. 2015 Feb 10; 112(6):E516-25. PMID: 25624474; PMCID: PMC4330758.
    45. Lindert S, Cheng Y, Kekenes-Huskey P, Regnier M, McCammon JA. Effects of HCM cTnI mutation R145G on troponin structure and modulation by PKA phosphorylation elucidated by molecular dynamics simulations. Biophys J. 2015 Jan 20; 108(2):395-407. PMID: 25606687; PMCID: PMC4302190.
    46. Wang N, Zhou S, Kekenes-Huskey PM, Li B, McCammon JA. Poisson-Boltzmann versus Size-Modified Poisson-Boltzmann Electrostatics Applied to Lipid Bilayers. J Phys Chem B. 2014 Dec 26; 118(51):14827-32. PMID: 25426875; PMCID: PMC4280115.
    47. Kim MO, Feng X, Feixas F, Zhu W, Lindert S, Bogue S, Sinko W, de Oliveira C, Rao G, Oldfield E, McCammon JA. A Molecular Dynamics Investigation of Mycobacterium tuberculosis Prenyl Synthases: Conformational Flexibility and Implications for Computer-aided Drug Discovery. Chem Biol Drug Des. 2015 Jun; 85(6):756-69. PMID: 25352216; PMCID: PMC4412765.
    48. Metzger VT, Eun C, Kekenes-Huskey PM, Huber G, McCammon JA. Electrostatic channeling in P. falciparum DHFR-TS: Brownian dynamics and Smoluchowski modeling. Biophys J. 2014 Nov 18; 107(10):2394-402. PMID: 25418308; PMCID: PMC4241442.
    49. Bertolini R, Goepfert C, Andrieu T, Nichols S, Walter MA, Frey FJ, McCammon JA, Frey BM. 18F-RB390: innovative ligand for imaging the T877A androgen receptor mutant in prostate cancer via positron emission tomography (PET). Prostate. 2015 Mar 01; 75(4):348-59. PMID: 25358634.
      View in: PubMed
    50. Lindert S, Tallorin L, Nguyen QG, Burkart MD, McCammon JA. In silico screening for Plasmodium falciparum enoyl-ACP reductase inhibitors. J Comput Aided Mol Des. 2015 Jan; 29(1):79-87. PMID: 25344312; PMCID: PMC4278936.
    51. Cheng Y, Lindert S, Kekenes-Huskey P, Rao VS, Solaro RJ, Rosevear PR, Amaro R, McCulloch AD, McCammon JA, Regnier M. Computational studies of the effect of the S23D/S24D troponin I mutation on cardiac troponin structural dynamics. Biophys J. 2014 Oct 07; 107(7):1675-85. PMID: 25296321; PMCID: PMC4190606.
    52. Tallorin LC, Durrant JD, Nguyen QG, McCammon JA, Burkart MD. Celastrol inhibits Plasmodium falciparum enoyl-acyl carrier protein reductase. Bioorg Med Chem. 2014 Nov 01; 22(21):6053-6061. PMID: 25284249.
      View in: PubMed
    53. Rao V, Cheng Y, Lindert S, Wang D, Oxenford L, McCulloch AD, McCammon JA, Regnier M. PKA phosphorylation of cardiac troponin I modulates activation and relaxation kinetics of ventricular myofibrils. Biophys J. 2014 Sep 02; 107(5):1196-1204. PMID: 25185555; PMCID: PMC4156663.
    54. Brown LM, Rogers KE, Aroonsakool N, McCammon JA, Insel PA. Allosteric inhibition of Epac: computational modeling and experimental validation to identify allosteric sites and inhibitors. J Biol Chem. 2014 Oct 17; 289(42):29148-57. PMID: 25183009; PMCID: PMC4200268.
    55. Kim MO, Blachly PG, Kaus JW, McCammon JA. Protocols utilizing constant pH molecular dynamics to compute pH-dependent binding free energies. J Phys Chem B. 2015 Jan 22; 119(3):861-72. PMID: 25134690; PMCID: PMC4306499.
    56. Boechi L, Pierce L, Komives EA, McCammon JA. Trypsinogen activation as observed in accelerated molecular dynamics simulations. Protein Sci. 2014 Nov; 23(11):1550-8. PMID: 25131668; PMCID: PMC4241106.
    57. Martin DP, Blachly PG, McCammon JA, Cohen SM. Exploring the influence of the protein environment on metal-binding pharmacophores. J Med Chem. 2014 Aug 28; 57(16):7126-35. PMID: 25116076; PMCID: PMC4148168.
    58. Blachly PG, Sandala GM, Giammona DA, Liu T, Bashford D, McCammon JA, Noodleman L. Use of Broken-Symmetry Density Functional Theory To Characterize the IspH Oxidized State: Implications for IspH Mechanism and Inhibition. J Chem Theory Comput. 2014 Sep 09; 10(9):3871-3884. PMID: 25221444.
      View in: PubMed
    59. Lindert S, Li MX, Sykes BD, McCammon JA. Computer-aided drug discovery approach finds calcium sensitizer of cardiac troponin. Chem Biol Drug Des. 2015 Feb; 85(2):99-106. PMID: 24954187; PMCID: PMC4456024.
    60. McCammon JA, Roux B, Voth G, Yang W. Special Issue on Free Energy. J Chem Theory Comput. 2014 Jul 08; 10(7):2631. PMID: 26586502.
      View in: PubMed
    61. Sinko W, Wang Y, Zhu W, Zhang Y, Feixas F, Cox CL, Mitchell DA, Oldfield E, McCammon JA. Undecaprenyl diphosphate synthase inhibitors: antibacterial drug leads. J Med Chem. 2014 Jul 10; 57(13):5693-701. PMID: 24827744.
      View in: PubMed
    62. Liu YL, Lindert S, Zhu W, Wang K, McCammon JA, Oldfield E. Taxodione and arenarone inhibit farnesyl diphosphate synthase by binding to the isopentenyl diphosphate site. Proc Natl Acad Sci U S A. 2014 Jun 24; 111(25):E2530-9. PMID: 24927548; PMCID: PMC4078810.
    63. Eun C, Ortiz-Sánchez JM, Da L, Wang D, McCammon JA. Molecular dynamics simulation study of conformational changes of transcription factor TFIIS during RNA polymerase II transcriptional arrest and reactivation. PLoS One. 2014; 9(5):e97975. PMID: 24842057; PMCID: PMC4026522.
    64. Kaus JW, Arrar M, McCammon JA. Accelerated adaptive integration method. J Phys Chem B. 2014 May 15; 118(19):5109-18. PMID: 24780083; PMCID: PMC4025579.
    65. Miao Y, Sinko W, Pierce L, Bucher D, Walker RC, McCammon JA. Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation. J Chem Theory Comput. 2014 Jul 08; 10(7):2677-2689. PMID: 25061441.
      View in: PubMed
    66. Martin DP, Blachly PG, Marts AR, Woodruff TM, de Oliveira CA, McCammon JA, Tierney DL, Cohen SM. 'Unconventional' coordination chemistry by metal chelating fragments in a metalloprotein active site. J Am Chem Soc. 2014 Apr 09; 136(14):5400-6. PMID: 24635441; PMCID: PMC4104174.
    67. Ivetac A, Swift SE, Boyer PL, Diaz A, Naughton J, Young JA, Hughes SH, McCammon JA. Discovery of novel inhibitors of HIV-1 reverse transcriptase through virtual screening of experimental and theoretical ensembles. Chem Biol Drug Des. 2014 May; 83(5):521-31. PMID: 24405985; PMCID: PMC3999242.
    68. Eun C, Kekenes-Huskey PM, Metzger VT, McCammon JA. A model study of sequential enzyme reactions and electrostatic channeling. J Chem Phys. 2014 Mar 14; 140(10):105101. PMID: 24628210; PMCID: PMC3977847.
    69. Götz AW, Bucher D, Lindert S, McCammon JA. Dipeptide Aggregation in Aqueous Solution from Fixed Point-Charge Force Fields. J Chem Theory Comput. 2014 Apr 08; 10(4):1631-1637. PMID: 24803868.
      View in: PubMed
    70. Zhou S, Cheng LT, Dzubiella J, Li B, McCammon JA. Variational Implicit Solvation with Poisson-Boltzmann Theory. J Chem Theory Comput. 2014 Apr 08; 10(4):1454-1467. PMID: 24803864.
      View in: PubMed
    71. Jacobitz AW, Wereszczynski J, Yi SW, Amer BR, Huang GL, Nguyen AV, Sawaya MR, Jung ME, McCammon JA, Clubb RT. Structural and computational studies of the Staphylococcus aureus sortase B-substrate complex reveal a substrate-stabilized oxyanion hole. J Biol Chem. 2014 Mar 28; 289(13):8891-902. PMID: 24519933; PMCID: PMC3979406.
    72. Lindert S, Maslennikov I, Chiu EJ, Pierce LC, McCammon JA, Choe S. Drug screening strategy for human membrane proteins: from NMR protein backbone structure to in silica- and NMR-screened hits. Biochem Biophys Res Commun. 2014 Mar 21; 445(4):724-33. PMID: 24525125; PMCID: PMC4457379.
    73. Brown LM, Rogers KE, McCammon JA, Insel PA. Identification and validation of modulators of exchange protein activated by cAMP (Epac) activity: structure-function implications for Epac activation and inhibition. J Biol Chem. 2014 Mar 21; 289(12):8217-30. PMID: 24497631; PMCID: PMC3961650.
    74. Guo Z, Li B, Dzubiella J, Cheng LT, McCammon JA, Che J. Heterogeneous Hydration of p53/MDM2 Complex. J Chem Theory Comput. 2014 Mar 11; 10(3):1302-1313. PMID: 24803860.
      View in: PubMed
    75. Miao Y, Nichols SE, McCammon JA. Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics. Phys Chem Chem Phys. 2014 Apr 14; 16(14):6398-406. PMID: 24445284; PMCID: PMC3960983.
    76. Miller B, Friedman AJ, Choi H, Hogan J, McCammon JA, Hook V, Gerwick WH. The marine cyanobacterial metabolite gallinamide A is a potent and selective inhibitor of human cathepsin L. J Nat Prod. 2014 Jan 24; 77(1):92-9. PMID: 24364476; PMCID: PMC3932306.
    77. Nguyen C, Haushalter RW, Lee DJ, Markwick PR, Bruegger J, Caldara-Festin G, Finzel K, Jackson DR, Ishikawa F, O'Dowd B, McCammon JA, Opella SJ, Tsai SC, Burkart MD. Trapping the dynamic acyl carrier protein in fatty acid biosynthesis. Nature. 2014 Jan 16; 505(7483):427-31. PMID: 24362570; PMCID: PMC4437705.
    78. Blachly PG, de Oliveira CA, Williams SL, McCammon JA. Utilizing a dynamical description of IspH to aid in the development of novel antimicrobial drugs. PLoS Comput Biol. 2013; 9(12):e1003395. PMID: 24367248; PMCID: PMC3868525.
    79. Feixas F, Lindert S, Sinko W, McCammon JA. Exploring the role of receptor flexibility in structure-based drug discovery. Biophys Chem. 2014 Feb; 186:31-45. PMID: 24332165; PMCID: PMC4459653.
    80. Kekenes-Huskey PM, Liao T, Gillette AK, Hake JE, Zhang Y, Michailova AP, McCulloch AD, McCammon JA. Molecular and subcellular-scale modeling of nucleotide diffusion in the cardiac myofilament lattice. Biophys J. 2013 Nov 05; 105(9):2130-40. PMID: 24209858; PMCID: PMC3835335.
    81. Miao Y, Nichols SE, McCammon JA. Mapping of allosteric druggable sites in activation-associated conformers of the M2 muscarinic receptor. Chem Biol Drug Des. 2014 Feb; 83(2):237-46. PMID: 24112716; PMCID: PMC4012891.
    82. Lindert S, Bucher D, Eastman P, Pande V, McCammon JA. Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units. J Chem Theory Comput. 2013 Nov 12; 9(11):4684-4691. PMID: 24634618.
      View in: PubMed
    83. Chan AH, Wereszczynski J, Amer BR, Yi SW, Jung ME, McCammon JA, Clubb RT. Discovery of Staphylococcus aureus sortase A inhibitors using virtual screening and the relaxed complex scheme. Chem Biol Drug Des. 2013 Oct; 82(4):418-28. PMID: 23701677; PMCID: PMC3841297.
    84. Boechi L, de Oliveira CA, Da Fonseca I, Kizjakina K, Sobrado P, Tanner JJ, McCammon JA. Substrate-dependent dynamics of UDP-galactopyranose mutase: Implications for drug design. Protein Sci. 2013 Nov; 22(11):1490-501. PMID: 23934860; PMCID: PMC3831665.
    85. Arrar M, de Oliveira CA, McCammon JA. Inactivating mutation in histone deacetylase 3 stabilizes its active conformation. Protein Sci. 2013 Oct; 22(10):1306-12. PMID: 23904210; PMCID: PMC3795489.
    86. Zhou S, Rogers KE, de Oliveira CA, Baron R, Cheng LT, Dzubiella J, Li B, McCammon JA. Variational Implicit-Solvent Modeling of Host-Guest Binding: A Case Study on Cucurbit[7]uril| J Chem Theory Comput. 2013 Sep 10; 9(9):4195-4204. PMID: 24039554.
      View in: PubMed
    87. Eun C, Kekenes-Huskey PM, McCammon JA. Influence of neighboring reactive particles on diffusion-limited reactions. J Chem Phys. 2013 Jul 28; 139(4):044117. PMID: 23901970; PMCID: PMC3745503.
    88. Bucher D, Hsu YH, Mouchlis VD, Dennis EA, McCammon JA. Insertion of the Ca²?-independent phospholipase A2 into a phospholipid bilayer via coarse-grained and atomistic molecular dynamics simulations. PLoS Comput Biol. 2013; 9(7):e1003156. PMID: 23935474; PMCID: PMC3723492.
    89. Zhao Y, Kwan YY, Che J, Li B, McCammon JA. Phase-field approach to implicit solvation of biomolecules with Coulomb-field approximation. J Chem Phys. 2013 Jul 14; 139(2):024111. PMID: 23862933; PMCID: PMC3724799.
    90. Durrant JD, Friedman AJ, Rogers KE, McCammon JA. Comparing neural-network scoring functions and the state of the art: applications to common library screening. J Chem Inf Model. 2013 Jul 22; 53(7):1726-35. PMID: 23734946; PMCID: PMC3735370.
    91. Sinko W, Miao Y, de Oliveira CA, McCammon JA. Population based reweighting of scaled molecular dynamics. J Phys Chem B. 2013 Oct 24; 117(42):12759-68. PMID: 23721224; PMCID: PMC3808002.
    92. Lindert S, Meiler J, McCammon JA. Iterative Molecular Dynamics-Rosetta Protein Structure Refinement Protocol to Improve Model Quality. J Chem Theory Comput. 2013 Aug 13; 9(8):3843-3847. PMID: 23956701.
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    93. Liao T, Zhang Y, Kekenes-Huskey PM, Cheng Y, Michailova A, McCulloch AD, Holst M, McCammon JA. Multi-core CPU or GPU-accelerated Multiscale Modeling for Biomolecular Complexes. Mol Based Math Biol. 2013 Jul; 1. PMID: 24352481.
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    94. Miao Y, Nichols SE, Gasper PM, Metzger VT, McCammon JA. Activation and dynamic network of the M2 muscarinic receptor. Proc Natl Acad Sci U S A. 2013 Jul 02; 110(27):10982-7. PMID: 23781107; PMCID: PMC3703993.
    95. Lindert S, Zhu W, Liu YL, Pang R, Oldfield E, McCammon JA. Farnesyl diphosphate synthase inhibitors from in silico screening. Chem Biol Drug Des. 2013 Jun; 81(6):742-8. PMID: 23421555; PMCID: PMC3671582.
    96. Wang N, Huber GA, McCammon JA. Assessing the two-body diffusion tensor calculated by the bead models. J Chem Phys. 2013 May 28; 138(20):204117. PMID: 23742464; PMCID: PMC3683057.
    97. Fuglestad B, Gasper PM, McCammon JA, Markwick PR, Komives EA. Correlated motions and residual frustration in thrombin. J Phys Chem B. 2013 Oct 24; 117(42):12857-63. PMID: 23621631; PMCID: PMC3808083.
    98. Durrant JD, Lindert S, McCammon JA. AutoGrow 3.0: an improved algorithm for chemically tractable, semi-automated protein inhibitor design. J Mol Graph Model. 2013 Jul; 44:104-12. PMID: 23792207; PMCID: PMC3842281.
    99. Nichols SE, Hernández CX, Wang Y, McCammon JA. Structure-based network analysis of an evolved G protein-coupled receptor homodimer interface. Protein Sci. 2013 Jun; 22(6):745-54. PMID: 23553730; PMCID: PMC3690714.
    100. Kim MO, Nichols SE, Wang Y, McCammon JA. Effects of histidine protonation and rotameric states on virtual screening of M. tuberculosis RmlC. J Comput Aided Mol Des. 2013 Mar; 27(3):235-46. PMID: 23579613; PMCID: PMC3639364.
    101. Baron R, McCammon JA. Molecular recognition and ligand association. Annu Rev Phys Chem. 2013; 64:151-75. PMID: 23473376.
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    102. Guerry P, Salmon L, Mollica L, Ortega Roldan JL, Markwick P, van Nuland NA, McCammon JA, Blackledge M. Mapping the population of protein conformational energy sub-states from NMR dipolar couplings. Angew Chem Int Ed Engl. 2013 Mar 11; 52(11):3181-5. PMID: 23371543.
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    103. Guo Z, Li B, Dzubiella J, Cheng LT, McCammon JA, Che J. Evaluation of Hydration Free Energy by Level-Set Variational Implicit-Solvent Model with Coulomb-Field Approximation. J Chem Theory Comput. 2013 Mar 12; 9(3):1778-1787. PMID: 23505345.
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    104. Hsu YH, Bucher D, Cao J, Li S, Yang SW, Kokotos G, Woods VL, McCammon JA, Dennis EA. Fluoroketone inhibition of Ca(2+)-independent phospholipase A2 through binding pocket association defined by hydrogen/deuterium exchange and molecular dynamics. J Am Chem Soc. 2013 Jan 30; 135(4):1330-7. PMID: 23256506; PMCID: PMC3561773.
    105. Setny P, Baron R, Michael Kekenes-Huskey P, McCammon JA, Dzubiella J. Solvent fluctuations in hydrophobic cavity-ligand binding kinetics. Proc Natl Acad Sci U S A. 2013 Jan 22; 110(4):1197-202. PMID: 23297241; PMCID: PMC3557044.
    106. Sinko W, Lindert S, McCammon JA. Accounting for receptor flexibility and enhanced sampling methods in computer-aided drug design. Chem Biol Drug Des. 2013 Jan; 81(1):41-9. PMID: 23253130; PMCID: PMC3540989.
    107. Zhu W, Zhang Y, Sinko W, Hensler ME, Olson J, Molohon KJ, Lindert S, Cao R, Li K, Wang K, Wang Y, Liu YL, Sankovsky A, de Oliveira CA, Mitchell DA, Nizet V, McCammon JA, Oldfield E. Antibacterial drug leads targeting isoprenoid biosynthesis. Proc Natl Acad Sci U S A. 2013 Jan 02; 110(1):123-8. PMID: 23248302; PMCID: PMC3538244.
    108. Arrar M, de Oliveira CA, Fajer M, Sinko W, McCammon JA. w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations. J Chem Theory Comput. 2013 Jan 08; 9(1):18-23. PMID: 23316122.
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    109. Kappel K, Wereszczynski J, Clubb RT, McCammon JA. The binding mechanism, multiple binding modes, and allosteric regulation of Staphylococcus aureus Sortase A probed by molecular dynamics simulations. Protein Sci. 2012 Dec; 21(12):1858-71. PMID: 23023444; PMCID: PMC3575916.
    110. Arrar M, Turnham R, Pierce L, de Oliveira CA, McCammon JA. Structural insight into the separate roles of inositol tetraphosphate and deacetylase-activating domain in activation of histone deacetylase 3. Protein Sci. 2013 Jan; 22(1):83-92. PMID: 23139175; PMCID: PMC3575863.
    111. Kekenes-Huskey PM, Lindert S, McCammon JA. Molecular basis of calcium-sensitizing and desensitizing mutations of the human cardiac troponin C regulatory domain: a multi-scale simulation study. PLoS Comput Biol. 2012; 8(11):e1002777. PMID: 23209387; PMCID: PMC3510055.
    112. Gasper PM, Fuglestad B, Komives EA, Markwick PR, McCammon JA. Allosteric networks in thrombin distinguish procoagulant vs. anticoagulant activities. Proc Natl Acad Sci U S A. 2012 Dec 26; 109(52):21216-22. PMID: 23197839; PMCID: PMC3535651.
    113. Kekenes-Huskey PM, Gillette A, Hake J, McCammon JA. Finite Element Estimation of Protein-Ligand Association Rates with Post-Encounter Effects: Applications to Calcium binding in Troponin C and SERCA. Comput Sci Discov. 2012 Oct 31; 5. PMID: 23293662.
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    114. Rogers KE, Ortiz-Sánchez JM, Baron R, Fajer M, de Oliveira CA, McCammon JA. On the Role of Dewetting Transitions in Host-Guest Binding Free Energy Calculations. J Chem Theory Comput. 2013 Jan 08; 9(1):46-53. PMID: 23316123.
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    115. Lindert S, Kekenes-Huskey PM, McCammon JA. Long-timescale molecular dynamics simulations elucidate the dynamics and kinetics of exposure of the hydrophobic patch in troponin C. Biophys J. 2012 Oct 17; 103(8):1784-9. PMID: 23083722; PMCID: PMC3475331.
    116. Lindert S, McCammon JA. Dynamics of Plasmodium falciparum enoyl-ACP reductase and implications on drug discovery. Protein Sci. 2012 Nov; 21(11):1734-45. PMID: 22969045; PMCID: PMC3527710.
    117. Kekenes-Huskey PM, Cheng Y, Hake JE, Sachse FB, Bridge JH, Holst MJ, McCammon JA, McCulloch AD, Michailova AP. Modeling effects of L-type ca(2+) current and na(+)-ca(2+) exchanger on ca(2+) trigger flux in rabbit myocytes with realistic T-tubule geometries. Front Physiol. 2012; 3:351. PMID: 23060801; PMCID: PMC3463892.
    118. Schlamadinger DE, Wang Y, McCammon JA, Kim JE. Spectroscopic and computational study of melittin, cecropin A, and the hybrid peptide CM15. J Phys Chem B. 2012 Sep 06; 116(35):10600-8. PMID: 22845179; PMCID: PMC3434763.
    119. Pierce LC, Salomon-Ferrer R, Augusto F de Oliveira C, McCammon JA, Walker RC. Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics. J Chem Theory Comput. 2012 Sep 11; 8(9):2997-3002. PMID: 22984356.
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    120. Konecny R, Baker NA, McCammon JA. iAPBS: a programming interface to Adaptive Poisson-Boltzmann Solver (APBS). Comput Sci Discov. 2012 Jul 26; 5(1). PMID: 22905037.
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    121. Ortiz-Sanchez JM, Nichols SE, Sayyah J, Brown JH, McCammon JA, Grant BJ. Identification of potential small molecule binding pockets on Rho family GTPases. PLoS One. 2012; 7(7):e40809. PMID: 22815826; PMCID: PMC3397943.
    122. Fuglestad B, Gasper PM, Tonelli M, McCammon JA, Markwick PR, Komives EA. The dynamic structure of thrombin in solution. Biophys J. 2012 Jul 03; 103(1):79-88. PMID: 22828334; PMCID: PMC3388214.
    123. Ortiz-Sánchez JM, Bucher D, Pierce LC, Markwick PR, McCammon JA. Exploring the Photophysical Properties of Molecular Systems Using Excited State Accelerated ab Initio Molecular Dynamics. J Chem Theory Comput. 2012 Aug 14; 8(8):2752-2761. PMID: 22904696.
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    124. Rogers KE, Keränen H, Durrant JD, Ratnam J, Doak A, Arkin MR, McCammon JA. Novel cruzain inhibitors for the treatment of Chagas' disease. Chem Biol Drug Des. 2012 Sep; 80(3):398-405. PMID: 22613098; PMCID: PMC3503458.
    125. Lindert S, Durrant JD, McCammon JA. LigMerge: a fast algorithm to generate models of novel potential ligands from sets of known binders. Chem Biol Drug Des. 2012 Sep; 80(3):358-65. PMID: 22594624; PMCID: PMC3462068.
    126. Salmon L, Pierce L, Grimm A, Ortega Roldan JL, Mollica L, Jensen MR, van Nuland N, Markwick PR, McCammon JA, Blackledge M. Multi-timescale conformational dynamics of the SH3 domain of CD2-associated protein using NMR spectroscopy and accelerated molecular dynamics. Angew Chem Int Ed Engl. 2012 Jun 18; 51(25):6103-6. PMID: 22565613; PMCID: PMC3541011.
    127. Friedman AJ, Durrant JD, Pierce LC, McCorvie TJ, Timson DJ, McCammon JA. The molecular dynamics of Trypanosoma brucei UDP-galactose 4'-epimerase: a drug target for African sleeping sickness. Chem Biol Drug Des. 2012 Aug; 80(2):173-81. PMID: 22487100; PMCID: PMC3399956.
    128. Wereszczynski J, McCammon JA. Nucleotide-dependent mechanism of Get3 as elucidated from free energy calculations. Proc Natl Acad Sci U S A. 2012 May 15; 109(20):7759-64. PMID: 22547793; PMCID: PMC3356667.
    129. Bauler P, Huber GA, McCammon JA. Hybrid finite element and Brownian dynamics method for diffusion-controlled reactions. J Chem Phys. 2012 Apr 28; 136(16):164107. PMID: 22559470; PMCID: PMC3350536.
    130. Hake J, Edwards AG, Yu Z, Kekenes-Huskey PM, Michailova AP, McCammon JA, Holst MJ, Hoshijima M, McCulloch AD. Modelling cardiac calcium sparks in a three-dimensional reconstruction of a calcium release unit. J Physiol. 2012 Sep 15; 590(18):4403-22. PMID: 22495592; PMCID: PMC3477749.
    131. Durrant JD, McCammon JA. AutoClickChem: click chemistry in silico. PLoS Comput Biol. 2012; 8(3):e1002397. PMID: 22438795; PMCID: PMC3305364.
    132. Wereszczynski J, McCammon JA. Simulations of the p97 complex suggest novel conformational states of hydrolysis intermediates. Protein Sci. 2012 Apr; 21(4):475-86. PMID: 22238181; PMCID: PMC3375748.
    133. Wang Y, Schlamadinger DE, Kim JE, McCammon JA. Comparative molecular dynamics simulations of the antimicrobial peptide CM15 in model lipid bilayers. Biochim Biophys Acta. 2012 May; 1818(5):1402-9. PMID: 22387432; PMCID: PMC3329965.
    134. Lawrenz M, Wereszczynski J, Ortiz-Sánchez JM, Nichols SE, McCammon JA. Thermodynamic integration to predict host-guest binding affinities. J Comput Aided Mol Des. 2012 May; 26(5):569-76. PMID: 22350568; PMCID: PMC4113475.
    135. Lindert S, Kekenes-Huskey PM, Huber G, Pierce L, McCammon JA. Dynamics and calcium association to the N-terminal regulatory domain of human cardiac troponin C: a multiscale computational study. J Phys Chem B. 2012 Jul 26; 116(29):8449-59. PMID: 22329450; PMCID: PMC3405770.
    136. Ivetac A, McCammon JA. A molecular dynamics ensemble-based approach for the mapping of druggable binding sites. Methods Mol Biol. 2012; 819:3-12. PMID: 22183526.
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    137. Nichols SE, Baron R, McCammon JA. On the use of molecular dynamics receptor conformations for virtual screening. Methods Mol Biol. 2012; 819:93-103. PMID: 22183532.
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    138. Holst M, McCammon JA, Yu Z, Zhou Y, Zhu Y. ADAPTIVE FINITE ELEMENT MODELING TECHNIQUES FOR THE POISSON-BOLTZMANN EQUATION. Commun Comput Phys. 2012; 11(1):179-214. PMID: 21949541.
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    139. Lawrenz M, Baron R, Wang Y, McCammon JA. Independent-Trajectory Thermodynamic Integration: a practical guide to protein-drug binding free energy calculations using distributed computing. Methods Mol Biol. 2012; 819:469-86. PMID: 22183552.
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    140. Sinko W, Sierecki E, de Oliveira CA, McCammon JA. Guide to virtual screening: application to the Akt phosphatase PHLPP. Methods Mol Biol. 2012; 819:561-73. PMID: 22183558.
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    141. Wereszczynski J, McCammon JA. Accelerated molecular dynamics in computational drug design. Methods Mol Biol. 2012; 819:515-24. PMID: 22183555.
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    142. Wang Z, Che J, Cheng LT, Dzubiella J, Li B, McCammon JA. Level-Set Variational Implicit-Solvent Modeling of Biomolecules with the Coulomb-Field Approximation. J Chem Theory Comput. 2012 Feb 14; 8(2):386-397. PMID: 22346739.
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    143. Grant BJ, Gheorghe DM, Zheng W, Alonso M, Huber G, Dlugosz M, McCammon JA, Cross RA. Electrostatically biased binding of kinesin to microtubules. PLoS Biol. 2011 Nov; 9(11):e1001207. PMID: 22140358; PMCID: PMC3226556.
    144. Sinko W, de Oliveira CA, Pierce LC, McCammon JA. Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations. J Chem Theory Comput. 2012 Jan 10; 8(1):17-23. PMID: 22241967.
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    145. Wereszczynski J, McCammon JA. Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition. Q Rev Biophys. 2012 Feb; 45(1):1-25. PMID: 22082669; PMCID: PMC3291752.
    146. McCammon JA. Gated Diffusion-controlled Reactions. BMC Biophys. 2011 Mar 02; 4:4. PMID: 21595999; PMCID: PMC3093672.
    147. Sander T, Frølund B, Bruun AT, Ivanov I, McCammon JA, Balle T. New insights into the GABA(A) receptor structure and orthosteric ligand binding: receptor modeling guided by experimental data. Proteins. 2011 May; 79(5):1458-77. PMID: 21365676; PMCID: PMC3076690.
    148. McCammon JA. Darwinian biophysics: electrostatics and evolution in the kinetics of molecular binding. Proc Natl Acad Sci U S A. 2009 May 12; 106(19):7683-4. PMID: 19416830; PMCID: PMC2683110.
    149. McCammon JA. Target flexibility in molecular recognition. Biochim Biophys Acta. 2005 Dec 30; 1754(1-2):221-4. PMID: 16181817.
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    150. McCammon JA. Theory of biomolecular recognition. Curr Opin Struct Biol. 1998 Apr; 8(2):245-9. PMID: 9631300.
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    151. Selawry OS, Neubauer HW, Selawry HS, Hoffmeister FS. Cholesteric thermography in tumors of the head and neck. Am J Surg. 1966 Oct; 112(4):537-40. PMID: 5915299.
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