PubRank

J A McCammon

Author PubWeight™ 255.28‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A 2001 42.14
2 Dynamics of folded proteins. Nature 1977 7.82
3 The statistical-thermodynamic basis for computation of binding affinities: a critical review. Biophys J 1997 7.64
4 Situs: A package for docking crystal structures into low-resolution maps from electron microscopy. J Struct Biol 1999 5.71
5 Prediction of pH-dependent properties of proteins. J Mol Biol 1994 4.99
6 The internal dynamics of globular proteins. CRC Crit Rev Biochem 1981 4.59
7 Dynamics of proteins: elements and function. Annu Rev Biochem 1983 4.56
8 Computer simulation of protein-protein association kinetics: acetylcholinesterase-fasciculin. J Mol Biol 1999 4.50
9 The determinants of pKas in proteins. Biochemistry 1996 3.45
10 Picosecond dynamics of tyrosine side chains in proteins. Biochemistry 1979 3.35
11 Computer simulations of actin polymerization can explain the barbed-pointed end asymmetry. J Mol Biol 1999 3.19
12 Dynamical theory of activated processes in globular proteins. Proc Natl Acad Sci U S A 1982 2.94
13 The hinge-bending mode in lysozyme. Nature 1976 2.78
14 Conformation gating as a mechanism for enzyme specificity. Proc Natl Acad Sci U S A 1998 2.61
15 Open "back door" in a molecular dynamics simulation of acetylcholinesterase. Science 1994 2.37
16 Thermodynamics and kinetics of actin filament nucleation. Biophys J 2001 2.34
17 Electrostatic influence on the kinetics of ligand binding to acetylcholinesterase. Distinctions between active center ligands and fasciculin. J Biol Chem 1997 2.31
18 Coupling hydrophobicity, dispersion, and electrostatics in continuum solvent models. Phys Rev Lett 2006 2.20
19 Water and polypeptide conformations in the gramicidin channel. A molecular dynamics study. Biophys J 1989 2.14
20 The structure of Sky1p reveals a novel mechanism for constitutive activity. Nat Struct Biol 2001 2.10
21 Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study. Biophys Chem 1999 2.07
22 Shedding light on the dark and weakly fluorescent states of green fluorescent proteins. Proc Natl Acad Sci U S A 1999 1.97
23 How electrolyte shielding influences the electrical potential in transmembrane ion channels. Biophys J 1989 1.97
24 Protein structural fluctuations during a period of 100 ps. Nature 1979 1.96
25 Simulation of enzyme-substrate encounter with gated active sites. Nat Struct Biol 1994 1.93
26 Coupling nonpolar and polar solvation free energies in implicit solvent models. J Chem Phys 2006 1.91
27 Time-correlation analysis of simulated water motion in flexible and rigid gramicidin channels. Biophys J 1991 1.91
28 Acetylcholinesterase: diffusional encounter rate constants for dumbbell models of ligand. Biophys J 1995 1.87
29 Accommodating protein flexibility in computational drug design. Mol Pharmacol 2000 1.84
30 Gating of the active site of triose phosphate isomerase: Brownian dynamics simulations of flexible peptide loops in the enzyme. Biophys J 1993 1.80
31 Hinge-bending in L-arabinose-binding protein. The "Venus's-flytrap" model. J Biol Chem 1982 1.80
32 Analysis of a 10-ns molecular dynamics simulation of mouse acetylcholinesterase. Biophys J 2001 1.78
33 Developing a dynamic pharmacophore model for HIV-1 integrase. J Med Chem 2000 1.71
34 Acetylcholinesterase: electrostatic steering increases the rate of ligand binding. Biochemistry 1993 1.69
35 Point charge distributions and electrostatic steering in enzyme/substrate encounter: Brownian dynamics of modified copper/zinc superoxide dismutases. Biochemistry 1990 1.67
36 Diffusion-controlled enzymatic reactions. Methods Enzymol 1991 1.66
37 Quasi-harmonic method for studying very low frequency modes in proteins. Biopolymers 1984 1.64
38 Kinetic mechanism of end-to-end annealing of actin filaments. J Mol Biol 2001 1.63
39 Molecular dynamics of ferrocytochrome c. Magnitude and anisotropy of atomic displacements. J Mol Biol 1981 1.60
40 Electrostatic and hydrodynamic orientational steering effects in enzyme-substrate association. Biophys J 1995 1.60
41 Annealing accounts for the length of actin filaments formed by spontaneous polymerization. Biophys J 1999 1.58
42 Identification of protein oligomerization states by analysis of interface conservation. Proc Natl Acad Sci U S A 2001 1.57
43 Molecular dynamics of ferrocytochrome c: anharmonicity of atomic displacements. Biopolymers 1982 1.56
44 Gated binding of ligands to proteins. Nature 1981 1.52
45 Dynamics of activated processes in globular proteins. Proc Natl Acad Sci U S A 1979 1.47
46 Theoretical calculation of relative binding affinity in host-guest systems. Proc Natl Acad Sci U S A 1986 1.46
47 Simulation of the diffusion-controlled reaction between superoxide and superoxide dismutase. II. Detailed models. Biopolymers 1988 1.45
48 Self-organizing neural networks bridge the biomolecular resolution gap. J Mol Biol 1998 1.45
49 Dewetting-controlled binding of ligands to hydrophobic pockets. Phys Rev Lett 2009 1.42
50 Molecular dynamics computations and solid state nuclear magnetic resonance of the gramicidin cation channel. Biophys J 1991 1.42
51 Electrostatic contributions to the stability of halophilic proteins. J Mol Biol 1998 1.42
52 Analysis of synaptic transmission in the neuromuscular junction using a continuum finite element model. Biophys J 1998 1.40
53 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 1.33
54 Internal motions of antibody molecules. Nature 1977 1.29
55 Multistep Brownian dynamics: application to short wormlike chains. Biopolymers 1984 1.26
56 Electrostatic channeling in the bifunctional enzyme dihydrofolate reductase-thymidylate synthase. J Mol Biol 1996 1.23
57 Internal mobility of ferrocytochrome c. Nature 1980 1.23
58 Evidence for electrostatic channeling in a fusion protein of malate dehydrogenase and citrate synthase. Biochemistry 1996 1.21
59 A molecular dynamics study of thermodynamic and structural aspects of the hydration of cavities in proteins. Biopolymers 1991 1.20
60 Acetylcholinesterase: role of the enzyme's charge distribution in steering charged ligands toward the active site. Biopolymers 1996 1.19
61 Simulation of charge-mutant acetylcholinesterases. Biochemistry 1995 1.18
62 Molecular dynamics of mouse acetylcholinesterase complexed with huperzine A. Biopolymers 1999 1.18
63 Poisson-Boltzmann analysis of the lambda repressor-operator interaction. Biophys J 1992 1.17
64 Calculation of weak protein-protein interactions: the pH dependence of the second virial coefficient. Biophys J 2001 1.15
65 Orientational steering in enzyme-substrate association: ionic strength dependence of hydrodynamic torque effects. Eur Biophys J 1996 1.13
66 Phenylalanine transfer RNA: molecular dynamics simulation. Science 1984 1.12
67 Mouse acetylcholinesterase unliganded and in complex with huperzine A: a comparison of molecular dynamics simulations. Biopolymers 1999 1.12
68 Molecular dynamics of ferrocytochrome c. Nature 1980 1.11
69 Correlation between rate of enzyme-substrate diffusional encounter and average Boltzmann factor around active site. Biopolymers 1998 1.10
70 Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids. Biopolymers 2006 1.08
71 Atomistic Brownian dynamics simulation of peptide phosphorylation. J Am Chem Soc 2001 1.07
72 Phosphorylation stabilizes the N-termini of alpha-helices. Biopolymers 1999 1.07
73 Modeling the electrophoresis of lysozyme. II. Inclusion of ion relaxation. Biophys J 1997 1.06
74 Molecular dynamics studies on the HIV-1 integrase catalytic domain. Biophys J 1999 1.06
75 Substrate concentration dependence of the diffusion-controlled steady-state rate constant. J Chem Phys 2005 1.05
76 The dynamics of proteins. Sci Am 1986 1.03
77 Simulation of the diffusion-controlled reaction between superoxide and superoxide dismutase. I. Simple models. Biopolymers 1985 1.02
78 Active site binding modes of HIV-1 integrase inhibitors. J Med Chem 2000 1.02
79 Theoretical study of hinge bending in L-arabinose-binding protein. Internal energy and free energy changes. J Biol Chem 1983 1.02
80 Simulation of biomolecular diffusion and complex formation. Biophys J 1986 1.01
81 Frictional properties of nonspherical multisubunit structures. Application to tubules and cylinders. Biopolymers 1976 1.01
82 Prediction of titration properties of structures of a protein derived from molecular dynamics trajectories. Protein Sci 1997 1.01
83 Intramolecular flexibility in phenylalanine transfer RNA. Nature 1981 1.00
84 Ordered water and ligand mobility in the HIV-1 integrase-5CITEP complex: a molecular dynamics study. J Med Chem 2001 1.00
85 Molecular dynamics simulations of the hyperthermophilic protein sac7d from Sulfolobus acidocaldarius: contribution of salt bridges to thermostability. J Mol Biol 1999 0.99
86 Enzyme-inhibitor association thermodynamics: explicit and continuum solvent studies. Biophys J 1997 0.99
87 Electrostatic channeling of substrates between enzyme active sites: comparison of simulation and experiment. Biochemistry 1997 0.98
88 Simulation methods for protein structure fluctuations. Biopolymers 1980 0.97
89 Molecular properties of amphotericin B membrane channel: a molecular dynamics simulation. Mol Pharmacol 1997 0.97
90 The hinge-bending mode of a lysozyme-inhibitor complex. Biopolymers 1986 0.97
91 Electrostatic effects in homeodomain-DNA interactions. J Mol Biol 1997 0.96
92 Large-amplitude bending motions in phenylalanine transfer RNA. Biopolymers 1984 0.96
93 Determinants of ligand binding to cAMP-dependent protein kinase. Biochemistry 1999 0.95
94 Quantum simulation of ferrocytochrome c. Nature 1988 0.95
95 Calculation of the pKa values for the ligands and side chains of Escherichia coli D-alanine:D-alanine ligase. J Med Chem 1999 0.94
96 Molecular dynamics of phenylalanine transfer RNA. J Biomol Struct Dyn 1983 0.93
97 Lateral diffusion of membrane proteins in the presence of static and dynamic corrals: suggestions for appropriate observables. Biophys J 2000 0.93
98 Acute metabolic responses in myxedema to large doses of intravenous L-thyroxine. Ann Intern Med 1972 0.92
99 Electrostatic steering of substrate to acetylcholinesterase: analysis of field fluctuations. Biopolymers 2000 0.91
100 Quantum-dynamical picture of a multistep enzymatic process: reaction catalyzed by phospholipase A(2). Biophys J 2000 0.91
101 Structure-based drug design: computational advances. Annu Rev Pharmacol Toxicol 1997 0.90
102 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 0.90
103 pH dependence of antibody/lysozyme complexation. Biochemistry 1997 0.90
104 Dynamical properties of fasciculin-2. Proteins 1999 0.89
105 Brownian and essential dynamics studies of the HIV-1 integrase catalytic domain. J Biomol Struct Dyn 1998 0.89
106 E230Q mutation of the catalytic subunit of cAMP-dependent protein kinase affects local structure and the binding of peptide inhibitor. Biopolymers 2006 0.89
107 Anti-insulin antibody structure and conformation. II. Molecular dynamics with explicit solvent. Biopolymers 1992 0.89
108 Inversion of receptor binding preferences by mutagenesis: free energy thermodynamic integration studies on sugar binding to L-arabinose binding proteins. Biochemistry 1993 0.88
109 Theoretical calculations of relative affinities of binding. Methods Enzymol 1991 0.88
110 Combined conformational search and finite-difference Poisson-Boltzmann approach for flexible docking. Application to an operator mutation in the lambda repressor-operator complex. J Mol Biol 1994 0.88
111 Study of global motions in proteins by weighted masses molecular dynamics: adenylate kinase as a test case. Proteins 1996 0.88
112 A model for enzyme-substrate interaction in alanine racemase. J Am Chem Soc 2001 0.88
113 Computer simulation study of the binding of an antiviral agent to a sensitive and a resistant human rhinovirus. J Comput Aided Mol Des 1989 0.88
114 Sidechain rotational isomerization in proteins. Dynamic simulation with solvent surroundings. Biophys J 1987 0.87
115 A virtual screening study of the acetylcholine binding protein using a relaxed-complex approach. Comput Biol Chem 2009 0.87
116 Statistical analysis of the fractal gating motions of the enzyme acetylcholinesterase. Phys Rev E Stat Nonlin Soft Matter Phys 2001 0.87
117 Molecular modeling methods. Basic techniques and challenging problems. Pharmacol Ther 1993 0.87
118 Binding of tacrine and 6-chlorotacrine by acetylcholinesterase. Biopolymers 1996 0.87
119 Determination of the pKa values of titratable groups of an antigen-antibody complex, HyHEL-5-hen egg lysozyme. Protein Eng 1995 0.86
120 Free energy simulations of the HyHEL-10/HEL antibody-antigen complex. Protein Eng 1995 0.86
121 "Semiempirical" models for biomembrane phase transitions and phase separations. J Am Chem Soc 1975 0.86
122 Poisson-Boltzmann model studies of molecular electrostatic properties of the cAMP-dependent protein kinase. Eur Biophys J 1999 0.86
123 Molecular-dynamics simulation of phenylalanine transfer RNA. II. Amplitudes, anisotropies, and anharmonicities of atomic motions. Biopolymers 1985 0.84
124 Molecular-dynamics simulation of phenylalanine transfer RNA. I. Methods and general results. Biopolymers 1985 0.84
125 Dynamic simulations of oxygen binding to myoglobin. Ann N Y Acad Sci 1986 0.84
126 Molecular dynamics studies of NMR relaxation in proteins. Biophys J 1980 0.83
127 Proton transfer dynamics of GART: the pH-dependent catalytic mechanism examined by electrostatic calculations. Protein Sci 2001 0.82
128 Simulation of electrostatic and hydrodynamic properties of Serratia endonuclease. Biopolymers 1997 0.81
129 Native-state conformational dynamics of GART: a regulatory pH-dependent coil-helix transition examined by electrostatic calculations. Protein Sci 2001 0.81
130 Kinase conformations: a computational study of the effect of ligand binding. Protein Sci 1997 0.81
131 Trajectory simulation studies of diffusion-controlled reactions. Faraday Discuss Chem Soc 1987 0.81
132 Superoxide dismutase: fluctuations in the structure and solvation of the active site channel studied by molecular dynamics simulation. Biopolymers 1989 0.81
133 Computational analysis of PKA-balanol interactions. J Med Chem 2001 0.80
134 Solvation studies of DMP323 and A76928 bound to HIV protease: analysis of water sites using grand canonical Monte Carlo simulations. Protein Sci 1998 0.80
135 Secondary structure prediction of the H5 pore of potassium channels. Protein Eng 1995 0.80
136 Internal dynamics of proteins. Short time and long time motions of aromatic sidechains in PTI. Biophys J 1980 0.78
137 A minimal model for stabilization of biomolecules by hydrocarbon cross-linking. J Chem Phys 2006 0.78
138 Finite element analysis of drug electrostatic diffusion: inhibition rate studies in N1 neuraminidase. Pac Symp Biocomput 2009 0.78
139 Quantum simulation of nuclear rearrangement in electron transfer reactions. Proc Natl Acad Sci U S A 1989 0.78
140 Anti-insulin antibody structure and conformation. I. Molecular modeling and mechanics of an insulin antibody. Biopolymers 1992 0.77
141 Apparent cooperativity in radioimmunoassay of human chorionic gonadotropin. Endocrinology 1973 0.77
142 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. J Mol Biol 1992 0.77
143 Symposium overview. Minnesota Conference on Supercomputing in Biology: Proteins, Nucleic Acids, and Water. J Comput Aided Mol Des 1988 0.77
144 Structural study of hinge bending in L-arabinose-binding protein. J Biol Chem 1984 0.76
145 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. J Mol Biol 1992 0.76
146 Fluctuation of the solvent-accessible surface area of tuna ferrocytochrome c. Biopolymers 1990 0.76
147 Computational science new horizons and relevance to pharmaceutical design. Trends Cardiovasc Med 1996 0.75
148 Conservative and nonconservative mutations in proteins: anomalous mutations in a transport receptor analyzed by free energy and quantum chemical calculations. Protein Sci 1995 0.75
149 Acetylcholinesterase: mechanisms of covalent inhibition of H447I mutant determined by computational analyses. Chem Biol Interact 2008 0.75
150 Association and dissociation kinetics of bobwhite quail lysozyme with monoclonal antibody HyHEL-5. Protein Eng 1999 0.75
151 Ionic association in water: from atoms to enzymes. Ann N Y Acad Sci 1986 0.75
152 Theoretical study of inhibition of adenosine deaminase by (8R)-coformycin and (8R)-deoxycoformycin. J Med Chem 1996 0.75
153 Atomic motions in phenylalanine transfer RNA probed by molecular dynamics simulations. Prog Clin Biol Res 1985 0.75
154 Colloquium on signaling and molecular structure in pharmacology (La Jolla, California, March 11-12, 1997). Mol Pharmacol 1997 0.75
155 Salt effects on enzyme-substrate interactions by Monte Carlo simulation. Ann N Y Acad Sci 1986 0.75
156 Repulsive interactions between polar and apolar atoms in globular proteins. J Mol Biol 1981 0.75