Published in Protein Sci on April 01, 2005
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Dead-end elimination with perturbations (DEEPer): a provable protein design algorithm with continuous sidechain and backbone flexibility. Proteins (2012) 1.11
The mechanism of domain alternation in the acyl-adenylate forming ligase superfamily member 4-chlorobenzoate: coenzyme A ligase. Biochemistry (2009) 1.07
The mechanism of ubiquitination in the cullin-RING E3 ligase machinery: conformational control of substrate orientation. PLoS Comput Biol (2009) 1.05
Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement. FEBS J (2014) 1.01
Exploring the energy landscapes of protein folding simulations with Bayesian computation. Biophys J (2012) 0.97
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Mechanism of action of cyclophilin a explored by metadynamics simulations. PLoS Comput Biol (2009) 0.86
Proline facilitates membrane insertion of the antimicrobial peptide maculatin 1.1 via surface indentation and subsequent lipid disordering. Biophys J (2013) 0.84
Improved atomistic Monte Carlo simulations demonstrate that poly-L-proline adopts heterogeneous ensembles of conformations of semi-rigid segments interrupted by kinks. J Phys Chem B (2012) 0.82
Tuning of thioredoxin redox properties by intramolecular hydrogen bonds. PLoS One (2013) 0.81
Efficient Parameter Estimation of Generalizable Coarse-Grained Protein Force Fields Using Contrastive Divergence: A Maximum Likelihood Approach. J Chem Theory Comput (2013) 0.76
Hydroxyproline Ring Pucker Causes Frustration of Helix Parameters in the Collagen Triple Helix. Sci Rep (2015) 0.75
Residue-centric modeling and design of saccharide and glycoconjugate structures. J Comput Chem (2016) 0.75
BioGPS descriptors for rational engineering of enzyme promiscuity and structure based bioinformatic analysis. PLoS One (2014) 0.75
Structure Motivator: a tool for exploring small three-dimensional elements in proteins. BMC Struct Biol (2012) 0.75
Beyond Antibodies: Development of a Novel Protein Scaffold Based on Human Chaperonin 10. Sci Rep (2016) 0.75
Mass & secondary structure propensity of amino acids explain their mutability and evolutionary replacements. Sci Rep (2017) 0.75
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Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods (2009) 3.25
Using quaternions to calculate RMSD. J Comput Chem (2004) 2.93
Binding of small-molecule ligands to proteins: "what you see" is not always "what you get". Structure (2009) 2.83
Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations. J Chem Theory Comput (2009) 2.53
Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent. J Phys Chem B (2007) 2.31
Predicting absolute ligand binding free energies to a simple model site. J Mol Biol (2007) 2.19
On the use of orientational restraints and symmetry corrections in alchemical free energy calculations. J Chem Phys (2006) 2.10
Assessment of protein structure refinement in CASP9. Proteins (2011) 2.06
A kinematic view of loop closure. J Comput Chem (2004) 2.03
Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site. J Mol Biol (2009) 1.90
How ions affect the structure of water. J Am Chem Soc (2002) 1.84
The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change. J Chem Theory Comput (2007) 1.73
Protein folding by zipping and assembly. Proc Natl Acad Sci U S A (2007) 1.72
Nonuniversal power law scaling in the probability distribution of scientific citations. Proc Natl Acad Sci U S A (2010) 1.66
Pulsating tubules from noncovalent macrocycles. Science (2012) 1.59
Assessment of the protein-structure refinement category in CASP8. Proteins (2009) 1.53
Treating entropy and conformational changes in implicit solvent simulations of small molecules. J Phys Chem B (2008) 1.47
Charge asymmetries in hydration of polar solutes. J Phys Chem B (2008) 1.45
Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J Mol Biol (2011) 1.40
Structural and spectroscopic studies of peptoid oligomers with alpha-chiral aliphatic side chains. J Am Chem Soc (2003) 1.39
A test on peptide stability of AMBER force fields with implicit solvation. J Phys Chem B (2008) 1.38
Ion pairing in molecular simulations of aqueous alkali halide solutions. J Phys Chem B (2009) 1.35
Surfaces affect ion pairing. J Phys Chem B (2005) 1.29
Protein loop modeling by using fragment assembly and analytical loop closure. Proteins (2010) 1.25
Predictions of hydration free energies from all-atom molecular dynamics simulations. J Phys Chem B (2009) 1.23
Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model. Protein Sci (2002) 1.21
Folding rates and low-entropy-loss routes of two-state proteins. J Mol Biol (2003) 1.21
Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins (2013) 1.20
Modeling aqueous solvation with semi-explicit assembly. Proc Natl Acad Sci U S A (2011) 1.20
Biomimetic nanostructures: creating a high-affinity zinc-binding site in a folded nonbiological polymer. J Am Chem Soc (2008) 1.19
Folding a nonbiological polymer into a compact multihelical structure. J Am Chem Soc (2005) 1.18
Teaching the principles of statistical dynamics. Am J Phys (2006) 1.17
The ultimate speed limit to protein folding is conformational searching. J Am Chem Soc (2007) 1.15
Cooperativity in two-state protein folding kinetics. Protein Sci (2004) 1.14
Theory for the three-dimensional Mercedes-Benz model of water. J Chem Phys (2009) 1.12
Maximum Caliber: a variational approach applied to two-state dynamics. J Chem Phys (2008) 1.11
Computing protein stabilities from their chain lengths. Proc Natl Acad Sci U S A (2009) 1.10
Oil/water transfer is partly driven by molecular shape, not just size. J Am Chem Soc (2010) 1.09
GalaxyWEB server for protein structure prediction and refinement. Nucleic Acids Res (2012) 1.08
GalaxyRefine: Protein structure refinement driven by side-chain repacking. Nucleic Acids Res (2013) 1.06
Blind prediction of charged ligand binding affinities in a model binding site. J Mol Biol (2013) 1.05
Folding very short peptides using molecular dynamics. PLoS Comput Biol (2006) 1.04
Fast protein folding kinetics. Proc Natl Acad Sci U S A (2003) 1.04
Folding kinetics of two-state proteins: effect of circularization, permutation, and crosslinks. J Mol Biol (2003) 1.04
Refinement of unreliable local regions in template-based protein models. Proteins (2012) 1.03
Scaffold topologies. 2. Analysis of chemical databases. J Chem Inf Model (2008) 1.02
Exploring zipping and assembly as a protein folding principle. Proteins (2007) 1.01
Transmembrane signaling of chemotaxis receptor tar: insights from molecular dynamics simulation studies. Biophys J (2011) 1.00
Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects. J Chem Phys (2013) 1.00
Blind test of physics-based prediction of protein structures. Biophys J (2009) 0.99
Computing the transition state populations in simple protein models. Biopolymers (2003) 0.99
Incorporation of chemoselective functionalities into peptoids via solid-phase submonomer synthesis. Bioconjug Chem (2004) 0.98
Predicting peptide structures in native proteins from physical simulations of fragments. PLoS Comput Biol (2009) 0.98
The FALC-Loop web server for protein loop modeling. Nucleic Acids Res (2011) 0.97
A maximum entropy framework for nonexponential distributions. Proc Natl Acad Sci U S A (2013) 0.97
Transition-states in protein folding kinetics: the structural interpretation of Phi values. J Mol Biol (2006) 0.96
Refinement of protein termini in template-based modeling using conformational space annealing. Proteins (2011) 0.95
Phi values in protein-folding kinetics have energetic and structural components. Proc Natl Acad Sci U S A (2005) 0.94
Scaffold topologies. 1. Exhaustive enumeration up to eight rings. J Chem Inf Model (2008) 0.93
GalaxyDock2: protein-ligand docking using beta-complex and global optimization. J Comput Chem (2013) 0.93
Simple liquid models with corrected dielectric constants. J Phys Chem B (2012) 0.92
GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions. BMC Bioinformatics (2012) 0.92
Testing the semi-explicit assembly solvation model in the SAMPL3 community blind test. J Comput Aided Mol Des (2011) 0.92
Routes are trees: the parsing perspective on protein folding. Proteins (2007) 0.92
MOPED: method for optimizing physical energy parameters using decoys. J Comput Chem (2003) 0.91
The stabilities of protein crystals. J Phys Chem B (2010) 0.91
Using motion planning to map protein folding landscapes and analyze folding kinetics of known native structures. J Comput Biol (2003) 0.91
Blind prediction of interfacial water positions in CAPRI. Proteins (2013) 0.90
Iterative assembly of helical proteins by optimal hydrophobic packing. Structure (2008) 0.90
Algorithmic dimensionality reduction for molecular structure analysis. J Chem Phys (2008) 0.90
Probing antibody internal dynamics with fluorescence anisotropy and molecular dynamics simulations. MAbs (2013) 0.89
Field-SEA: a model for computing the solvation free energies of nonpolar, polar, and charged solutes in water. J Phys Chem B (2013) 0.89
LigDockCSA: protein-ligand docking using conformational space annealing. J Comput Chem (2011) 0.88
Simulated evolution of protein-protein interaction networks with realistic topology. PLoS One (2012) 0.88
The elastic net algorithm and protein structure prediction. J Comput Chem (2002) 0.87
Development of an optimized activatable MMP-14 targeted SPECT imaging probe. Bioorg Med Chem (2008) 0.86
De novo protein structure prediction by dynamic fragment assembly and conformational space annealing. Proteins (2011) 0.86
GalaxyDock: protein-ligand docking with flexible protein side-chains. J Chem Inf Model (2012) 0.86
Cooperativity and specificity of Cys2His2 zinc finger protein-DNA interactions: a molecular dynamics simulation study. J Phys Chem B (2010) 0.85
Water's hydrogen bonds in the hydrophobic effect: a simple model. J Phys Chem B (2005) 0.85
Separated topologies--a method for relative binding free energy calculations using orientational restraints. J Chem Phys (2013) 0.85
Transition between B-DNA and Z-DNA: free energy landscape for the B-Z junction propagation. J Phys Chem B (2010) 0.84
GalaxyGemini: a web server for protein homo-oligomer structure prediction based on similarity. Bioinformatics (2013) 0.84
Markov processes follow from the principle of maximum caliber. J Chem Phys (2012) 0.84
General mechanism of two-state protein folding kinetics. J Am Chem Soc (2014) 0.83
Testing the semi-explicit assembly model of aqueous solvation in the SAMPL4 challenge. J Comput Aided Mol Des (2014) 0.83
Calculating the sensitivity and robustness of binding free energy calculations to force field parameters. J Chem Theory Comput (2013) 0.83
Strength of Calpha-H...O=C hydrogen bonds in transmembrane proteins. J Phys Chem B (2007) 0.83
Potential of mean force between two hydrophobic solutes in water. Biophys Chem (2002) 0.82
Statistical mechanics of helix bundles using a dynamic programming approach. J Am Chem Soc (2007) 0.82
A statistical mechanical theory for a two-dimensional model of water. J Chem Phys (2010) 0.82
A statistical rescoring scheme for protein-ligand docking: Consideration of entropic effect. Proteins (2008) 0.82
Comprehensive analysis of protein folding activation thermodynamics reveals a universal behavior violated by kinetically stable proteases. J Mol Biol (2005) 0.82
Simple model of hydrophobic hydration. J Phys Chem B (2012) 0.81