PubRank

Charles L Brooks

Author PubWeight™ 272.66‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem 2004 17.97
2 Improved treatment of the protein backbone in empirical force fields. J Am Chem Soc 2004 5.96
3 MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. J Mol Graph Model 2004 5.50
4 Recent advances in the development and application of implicit solvent models in biomolecule simulations. Curr Opin Struct Biol 2004 4.46
5 Generalized born model with a simple smoothing function. J Comput Chem 2003 4.36
6 Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. J Comput Chem 2004 3.83
7 New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations. J Comput Chem 2003 3.81
8 Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc Natl Acad Sci U S A 2003 3.64
9 Comparative study of several algorithms for flexible ligand docking. J Comput Aided Mol Des 2003 3.29
10 Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm. J Comput Chem 2003 3.27
11 Structure of the E. coli protein-conducting channel bound to a translating ribosome. Nature 2005 3.10
12 An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins. Biophys J 2003 2.91
13 The origins of asymmetry in the folding transition states of protein L and protein G. Protein Sci 2002 2.81
14 CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations. J Comput Chem 2004 2.80
15 CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. J Comput Chem 2004 2.79
16 Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM. J Struct Biol 2004 2.78
17 Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field. J Am Chem Soc 2006 2.59
18 Constant-pH molecular dynamics using continuous titration coordinates. Proteins 2004 2.52
19 Correlated motion and the effect of distal mutations in dihydrofolate reductase. Proc Natl Acad Sci U S A 2003 2.50
20 VIPERdb: a relational database for structural virology. Nucleic Acids Res 2006 2.46
21 Constant pH molecular dynamics with proton tautomerism. Biophys J 2005 2.44
22 Assessing scoring functions for protein-ligand interactions. J Med Chem 2004 2.41
23 VIPERdb2: an enhanced and web API enabled relational database for structural virology. Nucleic Acids Res 2008 2.38
24 Symmetry, form, and shape: guiding principles for robustness in macromolecular machines. Annu Rev Biophys Biomol Struct 2006 2.24
25 The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus. J Mol Biol 2002 2.24
26 Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism. Proc Natl Acad Sci U S A 2007 2.24
27 Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008. Nat Rev Drug Discov 2009 2.23
28 Recent advances in implicit solvent-based methods for biomolecular simulations. Curr Opin Struct Biol 2008 2.20
29 Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis. J Mol Biol 2004 2.19
30 The structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: lessons for protein design? Proc Natl Acad Sci U S A 2003 2.05
31 Ribosome assembly factors prevent premature translation initiation by 40S assembly intermediates. Science 2011 2.01
32 Implicit solvation based on generalized Born theory in different dielectric environments. J Chem Phys 2004 2.00
33 Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory. J Mol Biol 2002 1.98
34 Toward the accurate first-principles prediction of ionization equilibria in proteins. Biochemistry 2006 1.88
35 A modified TIP3P water potential for simulation with Ewald summation. J Chem Phys 2004 1.86
36 Can molecular dynamics simulations provide high-resolution refinement of protein structure? Proteins 2007 1.83
37 Selectivity in K+ channels is due to topological control of the permeant ion's coordinated state. Proc Natl Acad Sci U S A 2007 1.82
38 Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis. J Mol Biol 2005 1.81
39 Improved Gō-like models demonstrate the robustness of protein folding mechanisms towards non-native interactions. J Mol Biol 2003 1.76
40 Probing the folding free energy landscape of the Src-SH3 protein domain. Proc Natl Acad Sci U S A 2002 1.68
41 Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations. Proc Natl Acad Sci U S A 2005 1.66
42 Albumin binding to FcRn: distinct from the FcRn-IgG interaction. Biochemistry 2006 1.57
43 Deciphering the kinetic mechanism of spontaneous self-assembly of icosahedral capsids. Nano Lett 2007 1.56
44 Insights from coarse-grained Gō models for protein folding and dynamics. Int J Mol Sci 2009 1.52
45 Identifying native-like protein structures using physics-based potentials. J Comput Chem 2002 1.51
46 Application of torsion angle molecular dynamics for efficient sampling of protein conformations. J Comput Chem 2005 1.48
47 Linking folding with aggregation in Alzheimer's beta-amyloid peptides. Proc Natl Acad Sci U S A 2007 1.42
48 The coupling of structural fluctuations to hydride transfer in dihydrofolate reductase. Proteins 2004 1.37
49 The effects of ionic strength on protein stability: the cold shock protein family. J Mol Biol 2002 1.34
50 Model-free analysis of protein dynamics: assessment of accuracy and model selection protocols based on molecular dynamics simulation. J Biomol NMR 2004 1.32
51 Evolution and physics in comparative protein structure modeling. Acc Chem Res 2002 1.29
52 Structure, thermodynamics, and liquid-vapor equilibrium of ethanol from molecular-dynamics simulations using nonadditive interactions. J Chem Phys 2005 1.27
53 Ribosome motions modulate electrostatic properties. Biopolymers 2004 1.27
54 Molecular evolution of affinity and flexibility in the immune system. Proc Natl Acad Sci U S A 2007 1.26
55 Antibody evolution constrains conformational heterogeneity by tailoring protein dynamics. Proc Natl Acad Sci U S A 2006 1.26
56 Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions. Phys Chem Chem Phys 2007 1.25
57 Lambda-dynamics free energy simulation methods. J Comput Chem 2009 1.25
58 Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations. Biophys J 2006 1.23
59 MATCH: an atom-typing toolset for molecular mechanics force fields. J Comput Chem 2011 1.22
60 Exploring Flory's isolated-pair hypothesis: statistical mechanics of helix-coil transitions in polyalanine and the C-peptide from RNase A. Proc Natl Acad Sci U S A 2003 1.21
61 Coiled coils at the edge of configurational heterogeneity. Structural analyses of parallel and antiparallel homotetrameric coiled coils reveal configurational sensitivity to a single solvent-exposed amino acid substitution. Biochemistry 2006 1.21
62 De novo folding of membrane proteins: an exploration of the structure and NMR properties of the fd coat protein. J Mol Biol 2004 1.21
63 Integrating folding kinetics and protein function: biphasic kinetics and dual binding specificity in a WW domain. Proc Natl Acad Sci U S A 2004 1.21
64 A nonadditive methanol force field: bulk liquid and liquid-vapor interfacial properties via molecular dynamics simulations using a fluctuating charge model. J Chem Phys 2005 1.21
65 Invariant polymorphism in virus capsid assembly. J Am Chem Soc 2009 1.20
66 Peptide and protein folding and conformational equilibria: theoretical treatment of electrostatics and hydrogen bonding with implicit solvent models. Adv Protein Chem 2005 1.20
67 An electrostatic basis for the stability of thermophilic proteins. Proteins 2004 1.19
68 The 13 angstroms structure of a chaperonin GroEL-protein substrate complex by cryo-electron microscopy. J Mol Biol 2005 1.19
69 Exploring atomistic details of pH-dependent peptide folding. Proc Natl Acad Sci U S A 2006 1.17
70 Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent. J Chem Theory Comput 2012 1.17
71 The requirement for mechanical coupling between head and S2 domains in smooth muscle myosin ATPase regulation and its implications for dimeric motor function. J Mol Biol 2005 1.17
72 A general method to quantify quasi-equivalence in icosahedral viruses. J Mol Biol 2002 1.16
73 Evaluating CASP4 predictions with physical energy functions. Proteins 2002 1.14
74 Refinement of NMR structures using implicit solvent and advanced sampling techniques. J Am Chem Soc 2004 1.14
75 Critical importance of length-scale dependence in implicit modeling of hydrophobic interactions. J Am Chem Soc 2007 1.14
76 Removal of divalent cations induces structural transitions in red clover necrotic mosaic virus, revealing a potential mechanism for RNA release. J Virol 2006 1.14
77 An essential sensor histidine kinase controlled by transmembrane helix interactions with its auxiliary proteins. Proc Natl Acad Sci U S A 2008 1.13
78 Conformational substates modulate hydride transfer in dihydrofolate reductase. J Am Chem Soc 2005 1.13
79 Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling. J Biomol NMR 2005 1.12
80 How dihydrofolate reductase facilitates protonation of dihydrofolate. J Am Chem Soc 2003 1.11
81 Tryptophan side chain electrostatic interactions determine edge-to-face vs parallel-displaced tryptophan side chain geometries in the designed beta-hairpin "trpzip2". J Am Chem Soc 2005 1.11
82 Modern protein force fields behave comparably in molecular dynamics simulations. J Comput Chem 2002 1.11
83 Subdomain competition, cooperativity, and topological frustration in the folding of CheY. J Mol Biol 2008 1.10
84 3D maps of RNA interhelical junctions. Nat Protoc 2011 1.10
85 Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids. Biopolymers 2006 1.08
86 Conformational dynamics in human purine nucleoside phosphorylase with reactants and transition-state analogues. J Phys Chem B 2010 1.07
87 Exploring icosahedral virus structures with VIPER. Nat Rev Microbiol 2005 1.07
88 Chaperone activation by unfolding. Proc Natl Acad Sci U S A 2013 1.07
89 Folding intermediate in the villin headpiece domain arises from disruption of a N-terminal hydrogen-bonded network. J Am Chem Soc 2007 1.07
90 Deprotonation by dehydration: the origin of ammonium sensing in the AmtB channel. PLoS Comput Biol 2006 1.06
91 Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch. Nucleic Acids Res 2011 1.06
92 Statistical determinants of selective ionic complexation: ions in solvent, transport proteins, and other "hosts". Biophys J 2009 1.05
93 Detailed considerations for a balanced and broadly applicable force field: a study of substituted benzenes modeled with OPLS-AA. J Comput Chem 2005 1.05
94 pH-dependent dynamics of complex RNA macromolecules. J Chem Theory Comput 2013 1.05
95 Conformational change of the methionine 20 loop of Escherichia coli dihydrofolate reductase modulates pKa of the bound dihydrofolate. Protein Sci 2007 1.05
96 Cooperative and directional folding of the preQ1 riboswitch aptamer domain. J Am Chem Soc 2011 1.05
97 Hydrophobic cooperativity as a mechanism for amyloid nucleation. J Mol Biol 2007 1.04
98 Hierarchy of RNA functional dynamics. Annu Rev Biochem 2014 1.04
99 Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation. Curr Opin Struct Biol 2011 1.04
100 Revisiting the hexane-water interface via molecular dynamics simulations using nonadditive alkane-water potentials. J Chem Phys 2006 1.04
101 Application of solid-state NMR restraint potentials in membrane protein modeling. J Magn Reson 2008 1.03
102 Tilable nature of virus capsids and the role of topological constraints in natural capsid design. Phys Rev E Stat Nonlin Soft Matter Phys 2008 1.02
103 Harmonic Fourier beads method for studying rare events on rugged energy surfaces. J Chem Phys 2006 1.02
104 Native states of fast-folding proteins are kinetic traps. J Am Chem Soc 2013 1.01
105 Surveying implicit solvent models for estimating small molecule absolute hydration free energies. J Comput Chem 2011 1.00
106 K+/Na+ selectivity in toy cation binding site models is determined by the 'host'. Biophys J 2009 1.00
107 Probing pH-dependent dissociation of HdeA dimers. J Am Chem Soc 2011 1.00
108 Periodic table of virus capsids: implications for natural selection and design. PLoS One 2010 1.00
109 Mechanics of bacteriophage maturation. Proc Natl Acad Sci U S A 2012 1.00
110 Price to be paid for two-metal catalysis: magnesium ions that accelerate chemistry unavoidably limit product release from a protein kinase. J Am Chem Soc 2012 0.99
111 Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure. Nucleic Acids Res 2013 0.98
112 An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics. J Chem Theory Comput 2009 0.98
113 Ordering a dynamic protein via a small-molecule stabilizer. J Am Chem Soc 2013 0.97
114 Quantifying hub-like behavior in protein folding networks. J Chem Theory Comput 2012 0.97
115 A novel method to map and compare protein-protein interactions in spherical viral capsids. Proteins 2008 0.96
116 Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions. J Comput Chem 2008 0.96
117 Model of the toxic complex of anthrax: responsive conformational changes in both the lethal factor and the protective antigen heptamer. Protein Sci 2006 0.95
118 FoldGPCR: structure prediction protocol for the transmembrane domain of G protein-coupled receptors from class A. Proteins 2010 0.95
119 Computational simulations of the Trichoderma reesei cellobiohydrolase I acting on microcrystalline cellulose Ibeta: the enzyme-substrate complex. Carbohydr Res 2009 0.95
120 Synthesis and screening of a cyclic peptide library: discovery of small-molecule ligands against human prolactin receptor. Bioorg Med Chem 2008 0.95
121 On the equivalence point for ammonium (de)protonation during its transport through the AmtB channel. Biophys J 2007 0.95
122 Coarse grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulges. J Phys Chem B 2014 0.95
123 Revisiting the carboxylic acid dimers in aqueous solution: interplay of hydrogen bonding, hydrophobic interactions, and entropy. J Phys Chem B 2007 0.94
124 Characterizing the protonation state of cytosine in transient G·C Hoogsteen base pairs in duplex DNA. J Am Chem Soc 2013 0.94
125 Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations. J Comput Chem 2004 0.94
126 Determination of viral capsid elastic properties from equilibrium thermal fluctuations. Phys Rev Lett 2011 0.94
127 Predicting extreme pKa shifts in staphylococcal nuclease mutants with constant pH molecular dynamics. Proteins 2011 0.93
128 Molecular description of flexibility in an antibody combining site. J Phys Chem B 2010 0.93
129 New insights into the fundamental role of topological constraints as a determinant of two-way junction conformation. Nucleic Acids Res 2011 0.93
130 Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism. Proteins 2014 0.92
131 Exploring the symmetry and mechanism of virus capsid maturation via an ensemble of pathways. Biophys J 2012 0.92
132 WExplore: hierarchical exploration of high-dimensional spaces using the weighted ensemble algorithm. J Phys Chem B 2014 0.92
133 Topological frustration in beta alpha-repeat proteins: sequence diversity modulates the conserved folding mechanisms of alpha/beta/alpha sandwich proteins. J Mol Biol 2010 0.91
134 Receptor rigidity and ligand mobility in trypsin-ligand complexes. Proteins 2005 0.91
135 Using enhanced sampling and structural restraints to refine atomic structures into low-resolution electron microscopy maps. Structure 2012 0.90
136 Sekikaic acid and lobaric acid target a dynamic interface of the coactivator CBP/p300. Angew Chem Int Ed Engl 2012 0.90
137 On the morphology of viral capsids: elastic properties and buckling transitions. J Phys Chem B 2012 0.90
138 How to improve nature: study of the electrostatic properties of the surface of alpha-lactalbumin. Protein Eng Des Sel 2005 0.90
139 Improved model building and assessment of the Calcium-sensing receptor transmembrane domain. Proteins 2008 0.90
140 The importance of explicit chain representation in protein folding models: an examination of Ising-like models. Proteins 2003 0.90
141 Multiple intermediates, diverse conformations, and cooperative conformational changes underlie the catalytic hydride transfer reaction of dihydrofolate reductase. Top Curr Chem 2013 0.90
142 Generalized structural polymorphism in self-assembled viral particles. Nano Lett 2008 0.90
143 Viral capsid proteins are segregated in structural fold space. PLoS Comput Biol 2013 0.89
144 Gatekeepers in the ribosomal protein s6: thermodynamics, kinetics, and folding pathways revealed by a minimalist protein model. J Mol Biol 2004 0.89
145 Functional epitopes for site 1 of human prolactin. Biochemistry 2011 0.89
146 Multi-Site λ-dynamics for simulated Structure-Activity Relationship studies. J Chem Theory Comput 2011 0.89
147 Validating CHARMM parameters and exploring charge distribution rules in structure-based drug design. J Chem Theory Comput 2009 0.88
148 Viral capsid equilibrium dynamics reveals nonuniform elastic properties. Biophys J 2011 0.88
149 Towards Accurate Prediction of Protonation Equilibrium of Nucleic Acids. J Phys Chem Lett 2013 0.88
150 Site-specific hydration dynamics of globular proteins and the role of constrained water in solvent exchange with amphiphilic cosolvents. J Phys Chem B 2012 0.87
151 Conformational dynamics of a regulator of G-protein signaling protein reveals a mechanism of allosteric inhibition by a small molecule. ACS Chem Biol 2013 0.87
152 Alpha-lactalbumin unfolding is not sufficient to cause apoptosis, but is required for the conversion to HAMLET (human alpha-lactalbumin made lethal to tumor cells). Protein Sci 2003 0.87
153 Applying efficient implicit nongeometric constraints in alchemical free energy simulations. J Comput Chem 2011 0.86
154 Evaluation of several two-step scoring functions based on linear interaction energy, effective ligand size, and empirical pair potentials for prediction of protein-ligand binding geometry and free energy. J Chem Inf Model 2011 0.85
155 Geometric considerations in virus capsid size specificity, auxiliary requirements, and buckling. Proc Natl Acad Sci U S A 2009 0.85
156 Binding and folding of the small bacterial chaperone HdeA. J Phys Chem B 2013 0.85
157 Mechanism for ordered receptor binding by human prolactin. Biochemistry 2004 0.85
158 Crowding induced collective hydration of biological macromolecules over extended distances. J Am Chem Soc 2013 0.85
159 Selective complexation of K+ and Na+ in simple polarizable ion-ligating systems. J Am Chem Soc 2010 0.84
160 Deconstructing activation events in rhodopsin. J Am Chem Soc 2013 0.84
161 On the mechanism of crystalline polymorph selection by polymer heteronuclei. Langmuir 2011 0.84
162 pH-sensitive residues in the p19 RNA silencing suppressor protein from carnation Italian ringspot virus affect siRNA binding stability. Protein Sci 2013 0.84
163 Hexameric helicase deconstructed: interplay of conformational changes and substrate coupling. Biophys J 2010 0.84
164 Coevolution of function and the folding landscape: correlation with density of native contacts. Biophys J 2008 0.83
165 pH-induced stability switching of the bacteriophage HK97 maturation pathway. J Am Chem Soc 2014 0.82
166 PCASSO: a fast and efficient Cα-based method for accurately assigning protein secondary structure elements. J Comput Chem 2014 0.81
167 The high dielectric constant of staphylococcal nuclease is encoded in its structural architecture. J Am Chem Soc 2011 0.81
168 Functional impact of manipulation on the relative orientation of human prolactin receptor domains. Biochemistry 2011 0.81
169 Uncovering pH-dependent transient states of proteins with buried ionizable residues. J Am Chem Soc 2014 0.80
170 Obligate ordered binding of human lactogenic cytokines. J Biol Chem 2010 0.80
171 A universal trend among proteomes indicates an oily last common ancestor. PLoS Comput Biol 2012 0.79
172 Predicting structurally conserved contacts for homologous proteins using sequence conservation filters. Proteins 2009 0.79
173 Quantifying chaperone-mediated transitions in the proteostasis network of E. coli. PLoS Comput Biol 2013 0.79
174 The flexible C-terminal arm of the Lassa arenavirus Z-protein mediates interactions with multiple binding partners. Proteins 2010 0.79
175 Identification of residues outside the two binding sites that are critical for activation of the lactogenic activity of human growth hormone. J Biol Chem 2003 0.78
176 De novo prediction of the structures of M. tuberculosis membrane proteins. J Am Chem Soc 2008 0.78
177 Enhanced sampling and overfitting analyses in structural refinement of nucleic acids into electron microscopy maps. J Phys Chem B 2013 0.78
178 Different interfacial behaviors of peptides chemically immobilized on surfaces with different linker lengths and via different termini. J Phys Chem B 2014 0.77
179 Structure and function of a new class of human prolactin antagonists. Protein Expr Purif 2009 0.77
180 Predicting protein backbone chemical shifts from Cα coordinates: extracting high resolution experimental observables from low resolution models. J Chem Theory Comput 2015 0.77
181 Heterogeneous preferential solvation of water and trifluoroethanol in homologous lysozymes. J Phys Chem B 2014 0.77
182 Molecular structures of C- and N-terminus cysteine modified cecropin P1 chemically immobilized onto maleimide-terminated self-assembled monolayers investigated by molecular dynamics simulation. J Phys Chem B 2014 0.77
183 Noncanonical secondary structure stabilizes mitochondrial tRNA(Ser(UCN)) by reducing the entropic cost of tertiary folding. J Am Chem Soc 2015 0.77
184 pH-dependent transient conformational states control optical properties in cyan fluorescent protein. J Am Chem Soc 2015 0.77
185 Temperature-dependent behavior of protein-chromophore interactions: a theoretical study of a blue fluorescent antibody. Chemphyschem 2003 0.77
186 Steric and thermodynamic limits of design for the incorporation of large unnatural amino acids in aminoacyl-tRNA synthetase enzymes. Proteins 2010 0.77
187 A line integral reaction path approximation for large systems via nonlinear constrained optimization: application to alanine dipeptide and the beta hairpin of protein G. J Chem Phys 2006 0.76
188 A simple and fast approach for predicting (1)H and (13)C chemical shifts: toward chemical shift-guided simulations of RNA. J Phys Chem B 2014 0.76
189 Zinc binding to human lactogenic hormones and the human prolactin receptor. FEBS Lett 2011 0.76
190 Protein folding: with a little help... Nature 2002 0.75
191 Environmental effect on surface immobilized biological molecules. J Phys Chem B 2014 0.75
192 New paint and a new engine. J Comput Chem 2013 0.75