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Andrew McCammon

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

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Co-Publications
Name
14
Hamelberg, Donald
13
Gorfe, Alemayehu
13
Baker, Nathan
13
Shen, Tongye
13
Henchman, Richard
12
Trylska, Joanna
11
Briggs, James
11
Holst, Michael
10
Amaro, Rommie
10
Antosiewicz, Jan
10
Lu, Benzhuo
9
Wong, Chung
9
Taylor, Palmer
9
Chang, Chia-En
8
Straatsma, Tjerk

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Publications

TOP 3
Setny P; Wang Z; Cheng L-T; Li B; McCammon J A; Dzubiella J
Dewetting-controlled binding of ligands to hydrophobic pockets.
Cheng Li-Tien; Wang Zhongming; Setny Piotr; Dzubiella Joachim; Li Bo; McCammon J Andrew
Interfaces and hydrophobic interactions in receptor-ligand systems: A level-set variational implicit solvent approach.
Gorfe Alemayehu A; Lu Benzhuo; Yu Zeyun; McCammon J Andrew
Enzymatic activity versus structural dynamics: the case of acetylcholinesterase tetramer.

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All Publications

2009: Setny P; Wang Z; Cheng L-T; Li B; McCammon J A; Dzubiella J
Dewetting-controlled binding of ligands to hydrophobic pockets.
Physical review letters 2009;103(18):187801.
2009: Cheng Li-Tien; Wang Zhongming; Setny Piotr; Dzubiella Joachim; Li Bo; McCammon J Andrew
Interfaces and hydrophobic interactions in receptor-ligand systems: A level-set variational implicit solvent approach.
The Journal of chemical physics 2009;131(14):144102.
2009: Gorfe Alemayehu A; Lu Benzhuo; Yu Zeyun; McCammon J Andrew
Enzymatic activity versus structural dynamics: the case of acetylcholinesterase tetramer.
Biophysical journal 2009;97(3):897-905.
2009: Cervantes Carla F; Markwick Phineus R L; Sue Shih-Che; McCammon J Andrew; Dyson H Jane; Komives Elizabeth A
Functional dynamics of the folded ankyrin repeats of I kappa B alpha revealed by nuclear magnetic resonance.
Biochemistry 2009;48(33):8023-31.
2009: Knight James D R; Hamelberg Donald; McCammon J Andrew; Kothary Rashmi
The role of conserved water molecules in the catalytic domain of protein kinases.
Proteins 2009;76(3):527-35.
2009: Fajer Mikolai; Swift Robert V; McCammon J Andrew
Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamics.
Journal of computational chemistry 2009;30(11):1719-25.
2009: Baron Riccardo; Riley Conor; Chenprakhon Pirom; Thotsaporn Kittisak; Winter Remko T; Alfieri Andrea; Forneris Federico; van Berkel Willem J H; Chaiyen Pimchai; Fraaije Marco W; Mattevi Andrea; McCammon J Andrew
Multiple pathways guide oxygen diffusion into flavoenzyme active sites.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(26):10603-8.
2009: Cheng Xiaolin; Ivanov Ivaylo; Wang Hailong; Sine Steven M; McCammon J Andrew
Molecular-dynamics simulations of ELIC-a prokaryotic homologue of the nicotinic acetylcholine receptor.
Biophysical journal 2009;96(11):4502-13.
2009: Burke John E; Babakhani Arneh; Gorfe Alemayehu A; Kokotos George; Li Sheng; Woods Virgil L; McCammon J Andrew; Dennis Edward A
Location of inhibitors bound to group IVA phospholipase A2 determined by molecular dynamics and deuterium exchange mass spectrometry.
Journal of the American Chemical Society 2009;131(23):8083-91.
2009: McCammon J Andrew
Darwinian biophysics: electrostatics and evolution in the kinetics of molecular binding.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(19):7683-4.
2009: Wang Hai-Long; Toghraee Reza; Papke David; Cheng Xiao-Lin; McCammon J Andrew; Ravaioli Umberto; Sine Steven M
Single-channel current through nicotinic receptor produced by closure of binding site C-loop.
Biophysical journal 2009;96(9):3582-90.
2009: Ivetac Anthony; McCammon J Andrew
Elucidating the inhibition mechanism of HIV-1 non-nucleoside reverse transcriptase inhibitors through multicopy molecular dynamics simulations.
Journal of molecular biology 2009;388(3):644-58.
2009: Swift Robert V; McCammon J Andrew
Substrate induced population shifts and stochastic gating in the PBCV-1 mRNA capping enzyme.
Journal of the American Chemical Society 2009;131(14):5126-33.
2009: Amaro Rommie E; Cheng Xiaolin; Ivanov Ivaylo; Xu Dong; McCammon J Andrew
Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations.
Journal of the American Chemical Society 2009;131(13):4702-9.
2009: Babakhani Arneh; Talley Todd T; Taylor Palmer; McCammon J A
A virtual screening study of the acetylcholine binding protein using a relaxed-complex approach.
Computational biology and chemistry 2009;33(2):160-70.
2009: Xu Dong; Newhouse E Irene; Amaro Rommie E; Pao Hsing C; Cheng Lily S; Markwick Phineus R L; McCammon J Andrew; Li Wilfred W; Arzberger Peter W
Distinct glycan topology for avian and human sialopentasaccharide receptor analogues upon binding different hemagglutinins: a molecular dynamics perspective.
Journal of molecular biology 2009;387(2):465-91.
2009: Lu Shaoying; Michailova Anushka; Saucerman Jeffrey; Cheng Yuhui; Yu Zeyun; Kaiser Timothy; Li Wilfred; Bank Randolph; Holst Michael; McCammon J; Hayashi Takeharu; Hoshijima Masahiko; Arzberger Peter; McCulloch Andrew
Multiscale modeling in rodent ventricular myocytes.
IEEE engineering in medicine and biology magazine : the quarterly magazine of the Engineering in Medicine & Biology Society 2009;28(2):46-57.
2009: Grant Barry J; Gorfe Alemayehu A; McCammon J Andrew
Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics.
PLoS computational biology 2009;5(3):e1000325.
2009: Durrant Jacob D; Amaro Rommie E; McCammon J Andrew
AutoGrow: a novel algorithm for protein inhibitor design.
Chemical biology & drug design 2009;73(2):168-78.
2009: Agrawal Arpita; de Oliveira César Augusto F; Cheng Yuhui; Jacobsen Jennifer A; McCammon J Andrew; Cohen Seth M
Thioamide hydroxypyrothiones supersede amide hydroxypyrothiones in potency against anthrax lethal factor.
Journal of medicinal chemistry 2009;52(4):1063-74.
2009: Khavrutskii Ilja V; Gorfe Alemayehu A; Lu Benzhuo; McCammon J Andrew
Free energy for the permeation of Na(+) and Cl(-) ions and their ion-pair through a zwitterionic dimyristoyl phosphatidylcholine lipid bilayer by umbrella integration with harmonic fourier beads.
Journal of the American Chemical Society 2009;131(5):1706-16.
2009: Swift Robert V; Durrant Jacob; Amaro Rommie E; McCammon J Andrew
Toward understanding the conformational dynamics of RNA ligation.
Biochemistry 2009;48(4):709-19.
2009: Hamelberg Donald; McCammon J Andrew
Mechanistic insight into the role of transition-state stabilization in cyclophilin A.
Journal of the American Chemical Society 2009;131(1):147-52.
2009: Cheng Yuhui; Holst Michael J; McCammon J A
Finite element analysis of drug electrostatic diffusion: inhibition rate studies in N1 neuraminidase.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2009;():281-92.
2008: Yu Zeyun; Holst Michael J; Hayashi Takeharu; Bajaj Chandrajit L; Ellisman Mark H; McCammon J Andrew; Hoshijima Masahiko
Three-dimensional geometric modeling of membrane-bound organelles in ventricular myocytes: Bridging the gap between microscopic imaging and mathematical simulation.
Journal of structural biology 2008;164(3):304-13.
2008: Amaro Rommie E; Schnaufer Achim; Interthal Heidrun; Hol Wim; Stuart Kenneth D; McCammon J Andrew
Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(45):17278-83.
2008: Cheng Yuhui; Chang Chia-En A; Yu Zeyun; Zhang Yongjie; Sun Meihao; Leyh Thomas S; Holst Michael J; McCammon J Andrew
Diffusional channeling in the sulfate-activating complex: combined continuum modeling and coarse-grained brownian dynamics studies.
Biophysical journal 2008;95(10):4659-67.
2008: Wong Sergio E; Baron Riccardo; McCammon J Andrew
Hot-spot residues at the E9/Im9 interface help binding via different mechanisms.
Biopolymers 2008;89(11):916-20.
2008: Gorfe Alemayehu A; Baron Riccardo; McCammon J Andrew
Water-membrane partition thermodynamics of an amphiphilic lipopeptide: an enthalpy-driven hydrophobic effect.
Biophysical journal 2008;95(7):3269-77.
2008: Gorfe Alemayehu A; McCammon J Andrew
Similar membrane affinity of mono- and Di-S-acylated ras membrane anchors: a new twist in the role of protein lipidation.
Journal of the American Chemical Society 2008;130(38):12624-5.
2008: Cheng Y H; Cheng X L; Radic Z; McCammon J A
Acetylcholinesterase: mechanisms of covalent inhibition of H447I mutant determined by computational analyses.
Chemico-biological interactions 2008;175(1-3):196-9.
2008: Mura Cameron; McCammon J Andrew
Molecular dynamics of a kappaB DNA element: base flipping via cross-strand intercalative stacking in a microsecond-scale simulation.
Nucleic acids research 2008;36(15):4941-55.
2008: Amaro Rommie E; Baron Riccardo; McCammon J Andrew
An improved relaxed complex scheme for receptor flexibility in computer-aided drug design.
Journal of computer-aided molecular design 2008;22(9):693-705.
2008: Babakhani Arneh; Gorfe Alemayehu A; Kim Judy E; McCammon J Andrew
Thermodynamics of peptide insertion and aggregation in a lipid bilayer.
The journal of physical chemistry. B 2008;112(34):10528-34.
2008: Cheng Lily S; Amaro Rommie E; Xu Dong; Li Wilfred W; Arzberger Peter W; McCammon J Andrew
Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase.
Journal of medicinal chemistry 2008;51(13):3878-94.
2008: Gorfe Alemayehu A; Grant Barry J; McCammon J Andrew
Mapping the nucleotide and isoform-dependent structural and dynamical features of Ras proteins.
Structure (London, England : 1993) 2008;16(6):885-96.
2008: Yu Zeyun; Holst Michael J; Cheng Yuhui; McCammon J Andrew
Feature-preserving adaptive mesh generation for molecular shape modeling and simulation.
Journal of molecular graphics & modelling 2008;26(8):1370-80.
2008: Chang Chia-En A; McLaughlin William A; Baron Riccardo; Wang Wei; McCammon J Andrew
Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(21):7456-61.
2008: Baron Riccardo; McCammon J Andrew
(Thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding.
Chemphyschem : a European journal of chemical physics and physical chemistry 2008;9(7):983-8.
2008: Gunatilleke Shamila S; de Oliveira Cesar Augusto F; McCammon J Andrew; Barrios Amy M
Inhibition of cathepsin B by Au(I) complexes: a kinetic and computational study.
Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry 2008;13(4):555-61.
2008: Minh David D L; McCammon J Andrew
Springs and speeds in free energy reconstruction from irreversible single-molecule pulling experiments.
The journal of physical chemistry. B 2008;112(19):5892-7.
2008: Swift Robert V; McCammon J Andrew
Catalytically requisite conformational dynamics in the mRNA-capping enzyme probed by targeted molecular dynamics.
Biochemistry 2008;47(13):4102-11.
2008: Che Jianwei; Dzubiella Joachim; Li Bo; McCammon J Andrew
Electrostatic free energy and its variations in implicit solvent models.
The journal of physical chemistry. B 2008;112(10):3058-69.
2008: Abankwa Daniel; Hanzal-Bayer Michael; Ariotti Nicolas; Plowman Sarah J; Gorfe Alemayehu A; Parton Robert G; McCammon J Andrew; Hancock John F
A novel switch region regulates H-ras membrane orientation and signal output.
The EMBO journal 2008;27(5):727-35.
2008: Wang Hai-Long; Cheng Xiaolin; Taylor Palmer; McCammon J Andrew; Sine Steven M
Control of cation permeation through the nicotinic receptor channel.
PLoS computational biology 2008;4(2):e41.
2008: Landon Melissa R; Amaro Rommie E; Baron Riccardo; Ngan Chi Ho; Ozonoff David; McCammon J Andrew; Vajda Sandor
Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble.
Chemical biology & drug design 2008;71(2):106-16.
2008: Gorfe Alemayehu A; Chang Chia-en A; Ivanov Ivaylo; McCammon J Andrew
Dynamics of the acetylcholinesterase tetramer.
Biophysical journal 2008;94(4):1144-54.
2008: Khavrutskii Ilja V; Dzubiella Joachim; McCammon J Andrew
Computing accurate potentials of mean force in electrolyte solutions with the generalized gradient-augmented harmonic Fourier beads method.
The Journal of chemical physics 2008;128(4):044106.
2008: Zhou Y C; Lu Benzhuo; Huber Gary A; Holst Michael J; McCammon J Andrew
Continuum simulations of acetylcholine consumption by acetylcholinesterase: a Poisson-Nernst-Planck approach.
The journal of physical chemistry. B 2008;112(2):270-5.
2007: de Oliveira César Augusto F; Hamelberg Donald; McCammon J Andrew
Estimating kinetic rates from accelerated molecular dynamics simulations: alanine dipeptide in explicit solvent as a case study.
The Journal of chemical physics 2007;127(17):175105.
2007: Hamelberg Donald; de Oliveira César Augusto F; McCammon J Andrew
Sampling of slow diffusive conformational transitions with accelerated molecular dynamics.
The Journal of chemical physics 2007;127(15):155102.
2007: Cerutti David S; Baker Nathan A; McCammon J Andrew
Solvent reaction field potential inside an uncharged globular protein: a bridge between implicit and explicit solvent models?
The Journal of chemical physics 2007;127(15):155101.
2007: Minh David D L; Hamelberg Donald; McCammon J Andrew
Accelerated entropy estimates with accelerated dynamics.
The Journal of chemical physics 2007;127(15):154105.
2007: Lu Benzhuo; Zhou Y C; Huber Gary A; Bond Stephen D; Holst Michael J; McCammon J Andrew
Electrodiffusion: a continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution.
The Journal of chemical physics 2007;127(13):135102.
2007: Gorfe Alemayehu A; Babakhani Arneh; McCammon J Andrew
H-ras protein in a bilayer: interaction and structure perturbation.
Journal of the American Chemical Society 2007;129(40):12280-6.
2007: Cheng Xiaolin; Ivanov Ivaylo; Wang Hailong; Sine Steven M; McCammon J Andrew
Nanosecond-timescale conformational dynamics of the human alpha7 nicotinic acetylcholine receptor.
Biophysical journal 2007;93(8):2622-34.
2007: Khavrutskii Ilja V; McCammon J Andrew
Generalized gradient-augmented harmonic Fourier beads method with multiple atomic and/or center-of-mass positional restraints.
The Journal of chemical physics 2007;127(12):124901.
2007: Hamelberg Donald; Shen Tongye; McCammon J Andrew
A proposed signaling motif for nuclear import in mRNA processing via the formation of arginine claw.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(38):14947-51.
2007: Baron Riccardo; McCammon J Andrew
Dynamics, hydration, and motional averaging of a loop-gated artificial protein cavity: the W191G mutant of cytochrome c peroxidase in water as revealed by molecular dynamics simulations.
Biochemistry 2007;46(37):10629-42.
2007: Cheng Li-Tien; Dzubiella Joachim; McCammon J Andrew; Li Bo
Application of the level-set method to the implicit solvation of nonpolar molecules.
The Journal of chemical physics 2007;127(8):084503.
2007: Ivanov Ivaylo; Cheng Xiaolin; Sine Steven M; McCammon J Andrew
Barriers to ion translocation in cationic and anionic receptors from the Cys-loop family.
Journal of the American Chemical Society 2007;129(26):8217-24.
2007: Amaro Rommie E; Minh David D L; Cheng Lily S; Lindstrom William M; Olson Arthur J; Lin Jung-Hsin; Li Wilfred W; McCammon J Andrew
Remarkable loop flexibility in avian influenza N1 and its implications for antiviral drug design.
Journal of the American Chemical Society 2007;129(25):7764-5.
2007: Trylska Joanna; Tozzini Valentina; Chang Chia-en A; McCammon J Andrew
HIV-1 protease substrate binding and product release pathways explored with coarse-grained molecular dynamics.
Biophysical journal 2007;92(12):4179-87.
2007: Cheng Yuhui; Cheng Xiaolin; Radic Zoran; McCammon J Andrew
Acetylcholinesterase: mechanisms of covalent inhibition of wild-type and H447I mutant determined by computational analyses.
Journal of the American Chemical Society 2007;129(20):6562-70.
2007: Grant Barry J; McCammon J Andrew; Caves Leo S D; Cross Robert A
Multivariate analysis of conserved sequence-structure relationships in kinesins: coupling of the active site and a tubulin-binding sub-domain.
Journal of molecular biology 2007;368(5):1231-48.
2007: Sørensen Jesper; Hamelberg Donald; Schiøtt Birgit; McCammon J Andrew
Comparative MD analysis of the stability of transthyretin providing insight into the fibrillation mechanism.
Biopolymers 2007;86(1):73-82.
2007: Cheng Yuhui; Suen Jason K; Zhang Deqiang; Bond Stephen D; Zhang Yongjie; Song Yuhua; Baker Nathan A; Bajaj Chandrajit L; Holst Michael J; McCammon J Andrew
Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations.
Biophysical journal 2007;92(10):3397-406.
2007: Cheng Yuhui; Suen Jason K; Radic Zoran; Bond Stephen D; Holst Michael J; McCammon J Andrew
Continuum simulations of acetylcholine diffusion with reaction-determined boundaries in neuromuscular junction models.
Biophysical chemistry 2007;127(3):129-39.
2007: Tozzini Valentina; Trylska Joanna; Chang Chia-en; McCammon J Andrew
Flap opening dynamics in HIV-1 protease explored with a coarse-grained model.
Journal of structural biology 2007;157(3):606-15.
2007: Gorfe Alemayehu A; Hanzal-Bayer Michael; Abankwa Daniel; Hancock John F; McCammon J Andrew
Structure and dynamics of the full-length lipid-modified H-Ras protein in a 1,2-dimyristoylglycero-3-phosphocholine bilayer.
Journal of medicinal chemistry 2007;50(4):674-84.
2007: Leduc Philip R; Wong Michael S; Ferreira Placid M; Groff Richard E; Haslinger Kiryn; Koonce Michael P; Lee Woo Y; Love J Christopher; McCammon J Andrew; Monteiro-Riviere Nancy A; Rotello Vincent M; Rubloff Gary W; Westervelt Robert; Yoda Minami
Towards an in vivo biologically inspired nanofactory.
Nature nanotechnology 2007;2(1):3-7.
2007: Chang Chia-En A; Trylska Joanna; Tozzini Valentina; McCammon J Andrew
Binding pathways of ligands to HIV-1 protease: coarse-grained and atomistic simulations.
Chemical biology & drug design 2007;69(1):5-13.
2007: Ivanov Ivaylo; Tainer John A; McCammon J Andrew
Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(5):1465-70.
2007: Ngo Jacky Chi Ki; Gullingsrud Justin; Giang Kayla; Yeh Melinda Jean; Fu Xiang-Dong; Adams Joseph A; McCammon J Andrew; Ghosh Gourisankar
SR protein kinase 1 is resilient to inactivation.
Structure (London, England : 1993) 2007;15(1):123-33.
2007: de Oliveira Cesar Augusto F; Zissen Maurice; Mongon John; McCammon J Andrew
Molecular dynamics simulations of metalloproteinases types 2 and 3 reveal differences in the dynamic behavior of the S1' binding pocket.
Current pharmaceutical design 2007;13(34):3471-5.
2007: Amaro Rommie E; Swift Robert V; McCammon J Andrew
Functional and Structural Insights Revealed by Molecular Dynamics Simulations of an Essential RNA Editing Ligase in Trypanosoma brucei.
PLoS neglected tropical diseases 2007;1(2):e68.
2007: Gorfe Alemayehu A; Babakhani Arneh; McCammon J Andrew
Free energy profile of H-ras membrane anchor upon membrane insertion.
Angewandte Chemie (International ed. in English) 2007;46(43):8234-7.
2006: Lu Benzhuo; Cheng Xiaolin; Huang Jingfang; McCammon J Andrew
Order N algorithm for computation of electrostatic interactions in biomolecular systems.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(51):19314-9.
2006: de Oliveira César Augusto F; Hamelberg Donald; McCammon J Andrew
On the application of accelerated molecular dynamics to liquid water simulations.
The journal of physical chemistry. B 2006;110(45):22695-701.
2006: Grant Barry J; Rodrigues Ana P C; ElSawy Karim M; McCammon J Andrew; Caves Leo S D
Bio3d: an R package for the comparative analysis of protein structures.
Bioinformatics (Oxford, England) 2006;22(21):2695-6.
2006: Senapati Sanjib; Cheng Yuhui; McCammon J Andrew
In-situ synthesis of a tacrine-triazole-based inhibitor of acetylcholinesterase: configurational selection imposed by steric interactions.
Journal of medicinal chemistry 2006;49(21):6222-30.
2006: Bui Jennifer M; McCammon J Andrew
Protein complex formation by acetylcholinesterase and the neurotoxin fasciculin-2 appears to involve an induced-fit mechanism.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(42):15451-6.
2006: Cheng Xiaolin; Wang Hailong; Grant Barry; Sine Steven M; McCammon J Andrew
Targeted molecular dynamics study of C-loop closure and channel gating in nicotinic receptors.
PLoS computational biology 2006;2(9):e134.
2006: Hamelberg Donald; Shen Tongye; McCammon J Andrew
Insight into the role of hydration on protein dynamics.
The Journal of chemical physics 2006;125(9):094905.
2006: Jain Tushar; Cerutti David S; McCammon J Andrew
Configurational-bias sampling technique for predicting side-chain conformations in proteins.
Protein science : a publication of the Protein Society 2006;15(9):2029-39.
2006: Yang Grace; Trylska Joanna; Tor Yitzhak; McCammon J Andrew
Binding of aminoglycosidic antibiotics to the oligonucleotide A-site model and 30S ribosomal subunit: Poisson-Boltzmann model, thermal denaturation, and fluorescence studies.
Journal of medicinal chemistry 2006;49(18):5478-90.
2006: Lewis Jana A; Mongan John; McCammon J Andrew; Cohen Seth M
Evaluation and binding-mode prediction of thiopyrone-based inhibitors of anthrax lethal factor.
ChemMedChem 2006;1(7):694-7.
2006: Cerutti David S; Jain Tushar; McCammon J Andrew
CIRSE: a solvation energy estimator compatible with flexible protein docking and design applications.
Protein science : a publication of the Protein Society 2006;15(7):1579-96.
2006: Chang Chia-En; Shen Tongye; Trylska Joanna; Tozzini Valentina; McCammon J Andrew
Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model.
Biophysical journal 2006;90(11):3880-5.
2006: Perryman Alexander L; Lin Jung-Hsin; McCammon J Andrew
Restrained molecular dynamics simulations of HIV-1 protease: the first step in validating a new target for drug design.
Biopolymers 2006;82(3):272-84.
2006: Konecny Robert; Trylska Joanna; Tama Florence; Zhang Deqiang; Baker Nathan A; Brooks Charles L; McCammon J A
Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids.
Biopolymers 2006;82(2):106-20.
2006: Adcock Stewart A; McCammon J Andrew
Molecular dynamics: survey of methods for simulating the activity of proteins.
Chemical reviews 2006;106(5):1589-615.
2006: Minh David D L; Chang Chia-en; Trylska Joanna; Tozzini Valentina; McCammon J Andrew
The influence of macromolecular crowding on HIV-1 protease internal dynamics.
Journal of the American Chemical Society 2006;128(18):6006-7.
2006: Bui Jennifer M; Radic Zoran; Taylor Palmer; McCammon J Andrew
Conformational transitions in protein-protein association: binding of fasciculin-2 to acetylcholinesterase.
Biophysical journal 2006;90(9):3280-7.
2006: Shen Tongye; Hamelberg Donald; McCammon J Andrew
Elasticity of peptide omega bonds.
Physical review. E, Statistical, nonlinear, and soft matter physics 2006;73(4 Pt 1):041908.
2006: Hamacher K; Hübsch A; McCammon J A
A minimal model for stabilization of biomolecules by hydrocarbon cross-linking.
The Journal of chemical physics 2006;124(16):164907.
2006: Cheng Yuhui; Zhang Yingkai; McCammon J Andrew
How does activation loop phosphorylation modulate catalytic activity in the cAMP-dependent protein kinase: a theoretical study.
Protein science : a publication of the Protein Society 2006;15(4):672-83.
2006: Ung Man-Un; Lu Benzhuo; McCammon J A
E230Q mutation of the catalytic subunit of cAMP-dependent protein kinase affects local structure and the binding of peptide inhibitor.
Biopolymers 2006;81(6):428-39.
2006: Dzubiella J; Swanson J M J; McCammon J A
Coupling hydrophobicity, dispersion, and electrostatics in continuum solvent models.
Physical review letters 2006;96(8):087802.
2006: Zhang Deqiang; Gullingsrud Justin; McCammon J Andrew
Potentials of mean force for acetylcholine unbinding from the alpha7 nicotinic acetylcholine receptor ligand-binding domain.
Journal of the American Chemical Society 2006;128(9):3019-26.
2006: Dzubiella J; Swanson J M J; McCammon J A
Coupling nonpolar and polar solvation free energies in implicit solvent models.
The Journal of chemical physics 2006;124(8):084905.
2006: Hamacher Kay; Trylska Joanna; McCammon J Andrew
Dependency map of proteins in the small ribosomal subunit.
PLoS computational biology 2006;2(2):e10.
2006: Ivanov Ivaylo; Vemparala Satyavani; Pophristic Vojislava; Kuroda Kenichi; DeGrado William F; McCammon J Andrew; Klein Michael L
Characterization of nonbiological antimicrobial polymers in aqueous solution and at water-lipid interfaces from all-atom molecular dynamics.
Journal of the American Chemical Society 2006;128(6):1778-9.
2006: Gullingsrud Justin; Kim Choel; Taylor Susan S; McCammon J Andrew
Dynamic binding of PKA regulatory subunit RI alpha.
Structure (London, England : 1993) 2006;14(1):141-9.
2006: Vigil Dominico; Lin Jung-Hsin; Sotriffer Christoph A; Pennypacker Juniper K; McCammon J Andrew; Taylor Susan S
A simple electrostatic switch important in the activation of type I protein kinase A by cyclic AMP.
Protein science : a publication of the Protein Society 2006;15(1):113-21.
2006: Cheng Xiaolin; Lu Benzhuo; Grant Barry; Law Richard J; McCammon J Andrew
Channel opening motion of alpha7 nicotinic acetylcholine receptor as suggested by normal mode analysis.
Journal of molecular biology 2006;355(2):310-24.
2006: Giorgione Jennifer R; Lin Jung-Hsin; McCammon J Andrew; Newton Alexandra C
Increased membrane affinity of the C1 domain of protein kinase Cdelta compensates for the lack of involvement of its C2 domain in membrane recruitment.
The Journal of biological chemistry 2006;281(3):1660-9.
2006: Ivanov Ivaylo; Chapados Brian R; McCammon J Andrew; Tainer John A
Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications.
Nucleic acids research 2006;34(20):6023-33.
2005: Bui Jennifer M; McCammon J Andrew
Acetylcholinesterase: pivotal roles of its long omega loop (Cys69-Cys96) in regulating substrate binding.
Chemico-biological interactions 2005;157-158():357-9.
2005: Senapati Sanjib; Bui Jennifer M; McCammon J Andrew
Induced fit in mouse acetylcholinesterase upon binding a femtomolar inhibitor: a molecular dynamics study.
Journal of medicinal chemistry 2005;48(26):8155-62.
2005: Wong Chung F; Kua Jeremy; Zhang Yingkai; Straatsma T P; McCammon J Andrew
Molecular docking of balanol to dynamics snapshots of protein kinase A.
Proteins 2005;61(4):850-8.
2005: McCammon J Andrew
Target flexibility in molecular recognition.
Biochimica et biophysica acta 2005;1754(1-2):221-4.
2005: Zhang Deqiang; McCammon J Andrew
The association of tetrameric acetylcholinesterase with ColQ tail: a block normal mode analysis.
PLoS computational biology 2005;1(6):e62.
2005: Puerta David T; Mongan John; Tran Ba L; McCammon J Andrew; Cohen Seth M
Potent, selective pyrone-based inhibitors of stromelysin-1.
Journal of the American Chemical Society 2005;127(41):14148-9.
2005: Hamelberg Donald; McCammon J Andrew
Fast peptidyl cis-trans isomerization within the flexible Gly-rich flaps of HIV-1 protease.
Journal of the American Chemical Society 2005;127(40):13778-9.
2005: Minh David D L; Bui Jennifer M; Chang Chia-En; Jain Tushar; Swanson Jessica M J; McCammon J Andrew
The entropic cost of protein-protein association: a case study on acetylcholinesterase binding to fasciculin-2.
Biophysical journal 2005;89(4):L25-7.
2005: Shen Tongye; Zong Chenghang; Hamelberg Donald; McCammon J Andrew; Wolynes Peter G
The folding energy landscape and phosphorylation: modeling the conformational switch of the NFAT regulatory domain.
The FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2005;19(11):1389-95.
2005: Trylska Joanna; Tozzini Valentina; McCammon J Andrew
Exploring global motions and correlations in the ribosome.
Biophysical journal 2005;89(3):1455-63.
2005: Swanson Jessica M J; Mongan John; McCammon J Andrew
Limitations of atom-centered dielectric functions in implicit solvent models.
The journal of physical chemistry. B 2005;109(31):14769-72.
2005: Lu Benzhuo; Cheng Xiaolin; Hou Tingjun; McCammon J Andrew
Calculation of the Maxwell stress tensor and the Poisson-Boltzmann force on a solvated molecular surface using hypersingular boundary integrals.
The Journal of chemical physics 2005;123(8):084904.
2005: Trylska Joanna; McCammon J Andrew; Brooks Iii Charles L
Exploring assembly energetics of the 30S ribosomal subunit using an implicit solvent approach.
Journal of the American Chemical Society 2005;127(31):11125-33.
2005: Lu Benzhuo; Zhang Deqiang; McCammon J Andrew
Computation of electrostatic forces between solvated molecules determined by the Poisson-Boltzmann equation using a boundary element method.
The Journal of chemical physics 2005;122(21):214102.
2005: Dzubiella J; McCammon J A
Substrate concentration dependence of the diffusion-controlled steady-state rate constant.
The Journal of chemical physics 2005;122(18):184902.
2005: Law Richard J; Henchman Richard H; McCammon J Andrew
A gating mechanism proposed from a simulation of a human alpha7 nicotinic acetylcholine receptor.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(19):6813-8.
2005: Sims Peter A; Wong Chung F; Vuga Danka; McCammon J Andrew; Sefton Bartholomew M
Relative contributions of desolvation, inter- and intramolecular interactions to binding affinity in protein kinase systems.
Journal of computational chemistry 2005;26(7):668-81.
2005: Henchman Richard H; Wang Hai-Long; Sine Steven M; Taylor Palmer; McCammon J Andrew
Ligand-induced conformational change in the alpha7 nicotinic receptor ligand binding domain.
Biophysical journal 2005;88(4):2564-76.
2005: Zhang Deqiang; Suen Jason; Zhang Yongjie; Song Yuhua; Radic Zoran; Taylor Palmer; Holst Michael J; Bajaj Chandrajit; Baker Nathan A; McCammon J Andrew
Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods.
Biophysical journal 2005;88(3):1659-65.
2005: Gao Fan; Bren Nina; Burghardt Thomas P; Hansen Scott; Henchman Richard H; Taylor Palmer; McCammon J Andrew; Sine Steven M
Agonist-mediated conformational changes in acetylcholine-binding protein revealed by simulation and intrinsic tryptophan fluorescence.
The Journal of biological chemistry 2005;280(9):8443-51.
2005: Hamelberg Donald; Shen Tongye; McCammon J Andrew
Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: accelerated molecular dynamics analysis.
Journal of the American Chemical Society 2005;127(6):1969-74.
2005: Cheng Yuhui; Zhang Yingkai; McCammon J Andrew
How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: an ab initio QM/MM study.
Journal of the American Chemical Society 2005;127(5):1553-62.
2005: Lu Benzhuo; Wong Chung F; McCammon J Andrew
Release of ADP from the catalytic subunit of protein kinase A: a molecular dynamics simulation study.
Protein science : a publication of the Protein Society 2005;14(1):159-68.
2004: Mongan John; Case David A; McCammon J Andrew
Constant pH molecular dynamics in generalized Born implicit solvent.
Journal of computational chemistry 2004;25(16):2038-48.
2004: Zhang Deqiang; Konecny Robert; Baker Nathan A; McCammon J Andrew
Electrostatic interaction between RNA and protein capsid in cowpea chlorotic mottle virus simulated by a coarse-grain RNA model and a Monte Carlo approach.
Biopolymers 2004;75(4):325-37.
2004: Senapati Sanjib; Wong Chung F; McCammon J Andrew
Finite concentration effects on diffusion-controlled reactions.
The Journal of chemical physics 2004;121(16):7896-900.
2004: Trylska Joanna; Konecny Robert; Tama Florence; Brooks Charles L; McCammon J Andrew
Ribosome motions modulate electrostatic properties.
Biopolymers 2004;74(6):423-31.
2004: Sims Peter A; Wong Chung F; McCammon J Andrew
Charge optimization of the interface between protein kinases and their ligands.
Journal of computational chemistry 2004;25(11):1416-29.
2004: Dolinsky Todd J; Nielsen Jens E; McCammon J Andrew; Baker Nathan A
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations.
Nucleic acids research 2004;32(Web Server issue):W665-7.
2004: Hamelberg Donald; Mongan John; McCammon J Andrew
Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules.
The Journal of chemical physics 2004;120(24):11919-29.
2004: Hamelberg Donald; McCammon J Andrew
Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method.
Journal of the American Chemical Society 2004;126(24):7683-9.
2004: Bui Jennifer M; Tai Kaihsu; McCammon J Andrew
Acetylcholinesterase: enhanced fluctuations and alternative routes to the active site in the complex with fasciculin-2.
Journal of the American Chemical Society 2004;126(23):7198-205.
2004: Schames Julie R; Henchman Richard H; Siegel Jay S; Sotriffer Christoph A; Ni Haihong; McCammon J Andrew
Discovery of a novel binding trench in HIV integrase.
Journal of medicinal chemistry 2004;47(8):1879-81.
2004: Perryman Alexander L; Lin Jung-Hsin; McCammon J Andrew
HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs.
Protein science : a publication of the Protein Society 2004;13(4):1108-23.
2004: Song Yuhua; Zhang Yongjie; Shen Tongye; Bajaj Chandrajit L; McCammon J Andrew; Baker Nathan A
Finite element solution of the steady-state Smoluchowski equation for rate constant calculations.
Biophysical journal 2004;86(4):2017-29.
2004: Trylska Joanna; Grochowski Pawel; McCammon J Andrew
The role of hydrogen bonding in the enzymatic reaction catalyzed by HIV-1 protease.
Protein science : a publication of the Protein Society 2004;13(2):513-28.
2004: Swanson Jessica M J; Henchman Richard H; McCammon J Andrew
Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy.
Biophysical journal 2004;86(1 Pt 1):67-74.
2003: Kua Jeremy; Zhang Yingkai; Eslami Angelique C; Butler John R; McCammon J Andrew
Studying the roles of W86, E202, and Y337 in binding of acetylcholine to acetylcholinesterase using a combined molecular dynamics and multiple docking approach.
Protein science : a publication of the Protein Society 2003;12(12):2675-84.
2003: Henchman Richard H; Wang Hai-Long; Sine Steven M; Taylor Palmer; McCammon J Andrew
Asymmetric structural motions of the homomeric alpha7 nicotinic receptor ligand binding domain revealed by molecular dynamics simulation.
Biophysical journal 2003;85(5):3007-18.
2003: Cerutti David S; Wong Chung F; McCammon J Andrew
Brownian dynamics simulations of ion atmospheres around polyalanine and B-DNA: effects of biomolecular dielectric.
Biopolymers 2003;70(3):391-402.
2003: Shen Tongye; Wong Chung F; McCammon J Andrew
Brownian dynamics simulation of helix-capping motifs.
Biopolymers 2003;70(2):252-9.
2003: Bui Jennifer M; Henchman Richard H; McCammon J Andrew
The dynamics of ligand barrier crossing inside the acetylcholinesterase gorge.
Biophysical journal 2003;85(4):2267-72.
2003: Sept David; Baker Nathan A; McCammon J Andrew
The physical basis of microtubule structure and stability.
Protein science : a publication of the Protein Society 2003;12(10):2257-61.
2003: Morikis Dimitrios; Elcock Adrian H; Jennings Patricia A; McCammon J Andrew
The pH dependence of stability of the activation helix and the catalytic site of GART.
Biophysical chemistry 2003;105(2-3):279-91.
2003: Nielsen Jens Erik; McCammon J Andrew
Calculating pKa values in enzyme active sites.
Protein science : a publication of the Protein Society 2003;12(9):1894-901.
2003: Puerta David T; Schames Julie R; Henchman Richard H; McCammon J Andrew; Cohen Seth M
From model complexes to metalloprotein inhibition: a synergistic approach to structure-based drug discovery.
Angewandte Chemie (International ed. in English) 2003;42(32):3772-4.
2003: Shi Jianxin; Tai Kaihsu; McCammon J Andrew; Taylor Palmer; Johnson David A
Nanosecond dynamics of the mouse acetylcholinesterase cys69-cys96 omega loop.
The Journal of biological chemistry 2003;278(33):30905-11.
2003: Sims Peter A; Wong Chung F; McCammon J Andrew
A computational model of binding thermodynamics: the design of cyclin-dependent kinase 2 inhibitors.
Journal of medicinal chemistry 2003;46(15):3314-25.
2003: Tai Kaihsu; Bond Stephen D; MacMillan Hugh R; Baker Nathan Andrew; Holst Michael Jay; McCammon J Andrew
Finite element simulations of acetylcholine diffusion in neuromuscular junctions.
Biophysical journal 2003;84(4):2234-41.
2003: Nielsen Jens Erik; McCammon J Andrew
On the evaluation and optimization of protein X-ray structures for pKa calculations.
Protein science : a publication of the Protein Society 2003;12(2):313-26.
2003: Podtelezhnikov Alexei A; Gao Kui; Bushman Frederic D; McCammon J Andrew
Modeling HIV-1 integrase complexes based on their hydrodynamic properties.
Biopolymers 2003;68(1):110-20.
2003: Lin Jung-Hsin; Perryman Alexander L; Schames Julie R; McCammon J Andrew
The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme.
Biopolymers 2003;68(1):47-62.
2003: Baker Nathan A; McCammon J Andrew
Electrostatic interactions.
Methods of biochemical analysis 2003;44():427-40.
2003: Wong Chung F; McCammon J Andrew
Protein flexibility and computer-aided drug design.
Annual review of pharmacology and toxicology 2003;43():31-45.
2002: Perryman Alexander L; McCammon J Andrew
AutoDocking dinucleotides to the HIV-1 integrase core domain: exploring possible binding sites for viral and genomic DNA.
Journal of medicinal chemistry 2002;45(26):5624-7.
2002: Rowley David C; Hansen Mark S T; Rhodes Denise; Sotriffer Christoph A; Ni Haihong; McCammon J Andrew; Bushman Frederic D; Fenical William
Thalassiolins A-C: new marine-derived inhibitors of HIV cDNA integrase.
Bioorganic & medicinal chemistry 2002;10(11):3619-25.
2002: Lin Jung-Hsin; Baker Nathan A; McCammon J Andrew
Bridging implicit and explicit solvent approaches for membrane electrostatics.
Biophysical journal 2002;83(3):1374-9.
2002: Karplus Martin; McCammon J Andrew
Molecular dynamics simulations of biomolecules.
Nature structural biology 2002;9(9):646-52.
2002: Zhang Yingkai; Kua Jeremy; McCammon J Andrew
Role of the catalytic triad and oxyanion hole in acetylcholinesterase catalysis: an ab initio QM/MM study.
Journal of the American Chemical Society 2002;124(35):10572-7.
2002: Henchman Richard H; McCammon J Andrew
Structural and dynamic properties of water around acetylcholinesterase.
Protein science : a publication of the Protein Society 2002;11(9):2080-90.
2002: Shen Tongye; Canino Lawrence S; McCammon J Andrew
Unfolding proteins under external forces: a solvable model under the self-consistent pair contact probability approximation.
Physical review letters 2002;89(6):068103.
2002: Kua Jeremy; Zhang Yingkai; McCammon J Andrew
Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach.
Journal of the American Chemical Society 2002;124(28):8260-7.
2002: Henchman Richard H; McCammon J Andrew
Extracting hydration sites around proteins from explicit water simulations.
Journal of computational chemistry 2002;23(9):861-9.
2002: Shen Tongye; Tai Kaihsu; Henchman Richard H; McCammon J Andrew
Molecular dynamics of acetylcholinesterase.
Accounts of chemical research 2002;35(6):332-40.
2002: Tai Kaihsu; Shen Tongye; Henchman Richard H; Bourne Yves; Marchot Pascale; McCammon J Andrew
Mechanism of acetylcholinesterase inhibition by fasciculin: a 5-ns molecular dynamics simulation.
Journal of the American Chemical Society 2002;124(21):6153-61.
2002: Lin Jung-Hsin; Perryman Alexander L; Schames Julie R; McCammon J Andrew
Computational drug design accommodating receptor flexibility: the relaxed complex scheme.
Journal of the American Chemical Society 2002;124(20):5632-3.
2002: Henchman Richard H; Tai Kaihsu; Shen Tongye; McCammon J Andrew
Properties of water molecules in the active site gorge of acetylcholinesterase from computer simulation.
Biophysical journal 2002;82(5):2671-82.
2002: Ma Chiansan; Baker Nathan A; Joseph Simpson; McCammon J Andrew
Binding of aminoglycoside antibiotics to the small ribosomal subunit: a continuum electrostatics investigation.
Journal of the American Chemical Society 2002;124(7):1438-42.
2001: Morikis D; Elcock A H; Jennings P A; McCammon J A
Proton transfer dynamics of GART: the pH-dependent catalytic mechanism examined by electrostatic calculations.
Protein science : a publication of the Protein Society 2001;10(11):2379-92.
2001: Morikis D; Elcock A H; Jennings P A; McCammon J A
Native-state conformational dynamics of GART: a regulatory pH-dependent coil-helix transition examined by electrostatic calculations.
Protein science : a publication of the Protein Society 2001;10(11):2363-78.
2001: Ni H; Sotriffer C A; McCammon J A
Ordered water and ligand mobility in the HIV-1 integrase-5CITEP complex: a molecular dynamics study.
Journal of medicinal chemistry 2001;44(19):3043-7.
2001: Baker N A; Sept D; Joseph S; Holst M J; McCammon J A
Electrostatics of nanosystems: application to microtubules and the ribosome.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(18):10037-41.
2001: Tai K; Shen T; Börjesson U; Philippopoulos M; McCammon J A
Analysis of a 10-ns molecular dynamics simulation of mouse acetylcholinesterase.
Biophysical journal 2001;81(2):715-24.
2001: Wong C F; Hünenberger P H; Akamine P; Narayana N; Diller T; McCammon J A; Taylor S; Xuong N H
Computational analysis of PKA-balanol interactions.
Journal of medicinal chemistry 2001;44(10):1530-9.
2001: Shen T Y; Tai K; McCammon J A
Statistical analysis of the fractal gating motions of the enzyme acetylcholinesterase.
Physical review. E, Statistical, nonlinear, and soft matter physics 2001;63(4 Pt 1):041902.
2001: Elcock A H; McCammon J A
Identification of protein oligomerization states by analysis of interface conservation.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(6):2990-4.
2001: Nolen B; Yun C Y; Wong C F; McCammon J A; Fu X D; Ghosh G
The structure of Sky1p reveals a novel mechanism for constitutive activity.
Nature structural biology 2001;8(2):176-83.
2001: Elcock A H; McCammon J A
Calculation of weak protein-protein interactions: the pH dependence of the second virial coefficient.
Biophysical journal 2001;80(2):613-25.
2000: Sotriffer C A; Ni H; McCammon J A
Active site binding modes of HIV-1 integrase inhibitors.
Journal of medicinal chemistry 2000;43(22):4109-17.
2000: Bala P; Grochowski P; Nowinski K; Lesyng B; McCammon J A
Quantum-dynamical picture of a multistep enzymatic process: reaction catalyzed by phospholipase A(2).
Biophysical journal 2000;79(3):1253-62.
2000: Carlson H A; Masukawa K M; Rubins K; Bushman F D; Jorgensen W L; Lins R D; Briggs J M; McCammon J A
Developing a dynamic pharmacophore model for HIV-1 integrase.
Journal of medicinal chemistry 2000;43(11):2100-14.
2000: Brown F L; Leitner D M; McCammon J A; Wilson K R
Lateral diffusion of membrane proteins in the presence of static and dynamic corrals: suggestions for appropriate observables.
Biophysical journal 2000;78(5):2257-69.
2000: Carlson H A; McCammon J A
Accommodating protein flexibility in computational drug design.
Molecular pharmacology 2000;57(2):213-8.
1999: Sept D; Elcock A H; McCammon J A
Computer simulations of actin polymerization can explain the barbed-pointed end asymmetry.
Journal of molecular biology 1999;294(5):1181-9.
1999: Sept D; Xu J; Pollard T D; McCammon J A
Annealing accounts for the length of actin filaments formed by spontaneous polymerization.
Biophysical journal 1999;77(6):2911-9.
1999: Tara S; Helms V; Straatsma T P; McCammon J A
Molecular dynamics of mouse acetylcholinesterase complexed with huperzine A.
Biopolymers 1999;50(4):347-59.
1999: Baker N A; Helms V; McCammon J A
Dynamical properties of fasciculin-2.
Proteins 1999;36(4):447-53.
1999: Elcock A H; Gabdoulline R R; Wade R C; McCammon J A
Computer simulation of protein-protein association kinetics: acetylcholinesterase-fasciculin.
Journal of molecular biology 1999;291(1):149-62.
1999: Tara S; Straatsma T P; McCammon J A
Mouse acetylcholinesterase unliganded and in complex with huperzine A: a comparison of molecular dynamics simulations.
Biopolymers 1999;50(1):35-43.
1999: Lins R D; Briggs J M; Straatsma T P; Carlson H A; Greenwald J; Choe S; McCammon J A
Molecular dynamics studies on the HIV-1 integrase catalytic domain.
Biophysical journal 1999;76(6):2999-3011.
1999: Weber W; Helms V; McCammon J A; Langhoff P W
Shedding light on the dark and weakly fluorescent states of green fluorescent proteins.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(11):6177-82.
1999: Hünenberger P H; McCammon J A
Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study.
Biophysical chemistry 1999;78(1-2):69-88.
1999: Wriggers W; Milligan R A; McCammon J A
Situs: A package for docking crystal structures into low-resolution maps from electron microscopy.
Journal of structural biology 1999;125(2-3):185-95.
1999: Hünenberger P H; Helms V; Narayana N; Taylor S S; McCammon J A
Determinants of ligand binding to cAMP-dependent protein kinase.
Biochemistry 1999;38(8):2358-66.
1999: Carlson H A; Briggs J M; McCammon J A
Calculation of the pKa values for the ligands and side chains of Escherichia coli D-alanine:D-alanine ligase.
Journal of medicinal chemistry 1999;42(1):109-17.
1999: Blachut-Okrasinska E; Lesyng B; Briggs J M; McCammon J A; Antosiewicz J M
Poisson-Boltzmann model studies of molecular electrostatic properties of the cAMP-dependent protein kinase.
European biophysics journal : EBJ 1999;28(6):457-67.
1998: Weber W; Demirdjian H; Lins R D; Briggs J M; Ferreira R; McCammon J A
Brownian and essential dynamics studies of the HIV-1 integrase catalytic domain.
Journal of biomolecular structure & dynamics 1998;16(3):733-45.
1998: Wriggers W; Milligan R A; Schulten K; McCammon J A
Self-organizing neural networks bridge the biomolecular resolution gap.
Journal of molecular biology 1998;284(5):1247-54.
1998: Tara S; Elcock A H; Kirchhoff P D; Briggs J M; Radic Z; Taylor P; McCammon J A
Rapid binding of a cationic active site inhibitor to wild type and mutant mouse acetylcholinesterase: Brownian dynamics simulation including diffusion in the active site gorge.
Biopolymers 1998;46(7):465-74.
1998: Smart J L; McCammon J A
Analysis of synaptic transmission in the neuromuscular junction using a continuum finite element model.
Biophysical journal 1998;75(4):1679-88.
1998: Elcock A H; McCammon J A
Electrostatic contributions to the stability of halophilic proteins.
Journal of molecular biology 1998;280(4):731-48.
1998: Zhou H X; Briggs J M; Tara S; McCammon J A
Correlation between rate of enzyme-substrate diffusional encounter and average Boltzmann factor around active site.
Biopolymers 1998;45(5):355-60.
1998: Marrone T J; Resat H; Hodge C N; Chang C H; McCammon J A
Solvation studies of DMP323 and A76928 bound to HIV protease: analysis of water sites using grand canonical Monte Carlo simulations.
Protein science : a publication of the Protein Society 1998;7(3):573-9.
1997: Elcock A H; Huber G A; McCammon J A
Electrostatic channeling of substrates between enzyme active sites: comparison of simulation and experiment.
Biochemistry 1997;36(51):16049-58.
1997: Helms V; McCammon J A
Kinase conformations: a computational study of the effect of ligand binding.
Protein science : a publication of the Protein Society 1997;6(11):2336-43.
1997: Baginski M; Resat H; McCammon J A
Molecular properties of amphotericin B membrane channel: a molecular dynamics simulation.
Molecular pharmacology 1997;52(4):560-70.
1997: Taylor P; Ross E M; Sternweis P C; Neubig R R; McCammon J A
Colloquium on signaling and molecular structure in pharmacology (La Jolla, California, March 11-12, 1997).
Molecular pharmacology 1997;52(1):1-5.
1997: Antosiewicz J; Miller M D; Krause K L; McCammon J A
Simulation of electrostatic and hydrodynamic properties of Serratia endonuclease.
Biopolymers 1997;41(4):443-50.
1997: Fogolari F; Elcock A H; Esposito G; Viglino P; Briggs J M; McCammon J A
Electrostatic effects in homeodomain-DNA interactions.
Journal of molecular biology 1997;267(2):368-81.
1997: Wlodek S T; Antosiewicz J; McCammon J A
Prediction of titration properties of structures of a protein derived from molecular dynamics trajectories.
Protein science : a publication of the Protein Society 1997;6(2):373-82.
1997: Resat H; Marrone T J; McCammon J A
Enzyme-inhibitor association thermodynamics: explicit and continuum solvent studies.
Biophysical journal 1997;72(2 Pt 1):522-32.
1997: Marrone T J; Briggs J M; McCammon J A
Structure-based drug design: computational advances.
Annual review of pharmacology and toxicology 1997;37():71-90.
1996: McCammon J A
A speed limit for protein folding.
Proceedings of the National Academy of Sciences of the United States of America 1996;93(21):11426-7.
1996: Elcock A H; McCammon J A
Evidence for electrostatic channeling in a fusion protein of malate dehydrogenase and citrate synthase.
Biochemistry 1996;35(39):12652-8.
1996: Elcock A H; Potter M J; Matthews D A; Knighton D R; McCammon J A
Electrostatic channeling in the bifunctional enzyme dihydrofolate reductase-thymidylate synthase.
Journal of molecular biology 1996;262(3):370-4.
1996: Antosiewicz J; Wlodek S T; McCammon J A
Acetylcholinesterase: role of the enzyme's charge distribution in steering charged ligands toward the active site.
Biopolymers 1996;39(1):85-94.
1996: Antosiewicz J; McCammon J A; Gilson M K
The determinants of pKas in proteins.
Biochemistry 1996;35(24):7819-33.
1996: Elamrani S; Berry M B; Phillips G N; McCammon J A
Study of global motions in proteins by weighted masses molecular dynamics: adenylate kinase as a test case.
Proteins 1996;25(1):79-88.
1996: Wlodek S T; Antosiewicz J; McCammon J A; Straatsma T P; Gilson M K; Briggs J M; Humblet C; Sussman J L
Binding of tacrine and 6-chlorotacrine by acetylcholinesterase.
Biopolymers 1996;38(1):109-17.
1996: Marrone T J; Straatsma T P; Briggs J M; Wilson D K; Quiocho F A; McCammon J A
Theoretical study of inhibition of adenosine deaminase by (8R)-coformycin and (8R)-deoxycoformycin.
Journal of medicinal chemistry 1996;39(1):277-84.
1996: Antosiewicz J; Briggs J M; McCammon J A
Orientational steering in enzyme-substrate association: ionic strength dependence of hydrodynamic torque effects.
European biophysics journal : EBJ 1996;24(3):137-41.
1995: McDonald S M; Willson R C; McCammon J A
Determination of the pKa values of titratable groups of an antigen-antibody complex, HyHEL-5-hen egg lysozyme.
Protein engineering 1995;8(9):915-24.
1995: Pomès R; Willson R C; McCammon J A
Free energy simulations of the HyHEL-10/HEL antibody-antigen complex.
Protein engineering 1995;8(7):663-75.
1995: Antosiewicz J; McCammon J A
Electrostatic and hydrodynamic orientational steering effects in enzyme-substrate association.
Biophysical journal 1995;69(1):57-65.
1995: Antosiewicz J; McCammon J A; Wlodek S T; Gilson M K
Simulation of charge-mutant acetylcholinesterases.
Biochemistry 1995;34(13):4211-9.
1995: Cannon W R; Briggs J M; Shen J; McCammon J A; Quiocho F A
Conservative and nonconservative mutations in proteins: anomalous mutations in a transport receptor analyzed by free energy and quantum chemical calculations.
Protein science : a publication of the Protein Society 1995;4(3):387-93.
1995: Antosiewicz J; Gilson M K; Lee I H; McCammon J A
Acetylcholinesterase: diffusional encounter rate constants for dumbbell models of ligand.
Biophysical journal 1995;68(1):62-8.
1994: Zacharias M; Luty B A; Davis M E; McCammon J A
Combined conformational search and finite-difference Poisson-Boltzmann approach for flexible docking. Application to an operator mutation in the lambda repressor-operator complex.
Journal of molecular biology 1994;238(3):455-65.
1994: Antosiewicz J; McCammon J A; Gilson M K
Prediction of pH-dependent properties of proteins.
Journal of molecular biology 1994;238(3):415-36.
1994: Gilson M K; Straatsma T P; McCammon J A; Ripoll D R; Faerman C H; Axelsen P H; Silman I; Sussman J L
Open "back door" in a molecular dynamics simulation of acetylcholinesterase.
Science (New York, N.Y.) 1994;263(5151):1276-8.
1994: Wade R C; Luty B A; Demchuk E; Madura J D; Davis M E; Briggs J M; McCammon J A
Simulation of enzyme-substrate encounter with gated active sites.
Nature structural biology 1994;1(1):65-9.
1993: Lesyng B; McCammon J A
Molecular modeling methods. Basic techniques and challenging problems.
Pharmacology & therapeutics 1993;60(2):149-67.
1993: Zacharias M; Straatsma T P; McCammon J A; Quiocho F A
Inversion of receptor binding preferences by mutagenesis: free energy thermodynamic integration studies on sugar binding to L-arabinose binding proteins.
Biochemistry 1993;32(29):7428-34.
1993: Wade R C; Davis M E; Luty B A; Madura J D; McCammon J A
Gating of the active site of triose phosphate isomerase: Brownian dynamics simulations of flexible peptide loops in the enzyme.
Biophysical journal 1993;64(1):9-15.
1993: Tan R C; Truong T N; McCammon J A; Sussman J L
Acetylcholinesterase: electrostatic steering increases the rate of ligand binding.
Biochemistry 1993;32(2):401-3.
1992: Zacharias M; Luty B A; Davis M E; McCammon J A
Poisson-Boltzmann analysis of the lambda repressor-operator interaction.
Biophysical journal 1992;63(5):1280-5.
1992: Wade R C; McCammon J A
Binding of an antiviral agent to a sensitive and a resistant human rhinovirus. Computer simulation studies with sampling of amino acid side-chain conformations. II. Calculation of free-energy differences by thermodynamic integration.
Journal of molecular biology 1992;225(3):697-712.
1992: Wade R C; McCammon J A
Binding of an antiviral agent to a sensitive and a resistant human rhinovirus. Computer simulation studies with sampling of amino acid side-chain conformation. I. Mapping the rotamers of residue 188 of viral protein 1.
Journal of molecular biology 1992;225(3):679-96.
1992: Tanner J J; Nell L J; McCammon J A
Anti-insulin antibody structure and conformation. II. Molecular dynamics with explicit solvent.
Biopolymers 1992;32(1):23-32.
1992: Nell L J; McCammon J A; Subramaniam S
Anti-insulin antibody structure and conformation. I. Molecular modeling and mechanics of an insulin antibody.
Biopolymers 1992;32(1):11-21.
1991: Wade R C; Mazor M H; McCammon J A; Quiocho F A
A molecular dynamics study of thermodynamic and structural aspects of the hydration of cavities in proteins.
Biopolymers 1991;31(8):919-31.
1991: Davis M E; Madura J D; Sines J; Luty B A; Allison S A; McCammon J A
Diffusion-controlled enzymatic reactions.
Methods in enzymology 1991;202():473-97.
1990: Zheng C; Wong C F; McCammon J A
Fluctuation of the solvent-accessible surface area of tuna ferrocytochrome c.
Biopolymers 1990;29(14):1877-83.
1988: Zheng C; Wong C F; McCammon J A; Wolynes P G
Quantum simulation of ferrocytochrome c.
Nature 1988;334(6184):726-8.
1987: McCammon J A
Computer-aided molecular design.
Science (New York, N.Y.) 1987;238(4826):486-91.

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