Published in Commun Comput Phys on December 06, 2012
Parameterization for molecular Gaussian surface and a comparison study of surface mesh generation. J Mol Model (2015) 0.88
Influence of Grid Spacing in Poisson-Boltzmann Equation Binding Energy Estimation. J Chem Theory Comput (2013) 0.88
A general and robust ray-casting-based algorithm for triangulating surfaces at the nanoscale. PLoS One (2013) 0.88
Progress in developing Poisson-Boltzmann equation solvers. Mol Based Math Biol (2013) 0.84
Multiscale geometric modeling of macromolecules II: Lagrangian representation. J Comput Chem (2013) 0.82
Implicit solvent methods for free energy estimation. Eur J Med Chem (2014) 0.78
Accuracy of continuum electrostatic calculations based on three common dielectric boundary definitions. J Theor Comput Chem (2014) 0.78
A combined MPI-CUDA parallel solution of linear and nonlinear Poisson-Boltzmann equation. Biomed Res Int (2014) 0.75
The interpretation of protein structures: estimation of static accessibility. J Mol Biol (1971) 40.24
Reduced surface: an efficient way to compute molecular surfaces. Biopolymers (1996) 10.62
Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects. J Comput Chem (2002) 5.18
Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape. Proteins (1998) 3.44
Effective Born radii in the generalized Born approximation: the importance of being perfect. J Comput Chem (2002) 3.06
Internal cavities and buried waters in globular proteins. Biochemistry (1986) 2.40
The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology. J Mol Recognit (2002) 2.20
Quality Meshing of Implicit Solvation Models of Biomolecular Structures. Comput Aided Geom Des (2006) 1.96
VORO++: a three-dimensional voronoi cell library in C++. Chaos (2009) 1.88
Potentials of mean force between ionizable amino acid side chains in water. J Am Chem Soc (2003) 1.65
Minimal molecular surfaces and their applications. J Comput Chem (2008) 1.57
Generating triangulated macromolecular surfaces by Euclidean Distance Transform. PLoS One (2009) 1.54
Efficient molecular surface generation using level-set methods. J Mol Graph Model (2006) 1.35
Limitations of atom-centered dielectric functions in implicit solvent models. J Phys Chem B (2005) 1.31
SIMS: computation of a smooth invariant molecular surface. Biophys J (1997) 1.24
The contour-buildup algorithm to calculate the analytical molecular surface. J Struct Biol (1996) 1.00
MetaMol: high-quality visualization of molecular skin surface. J Mol Graph Model (2008) 0.94
Numerical integration techniques for curved-element discretizations of molecule-solvent interfaces. J Chem Phys (2007) 0.89
Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects. J Comput Chem (2002) 5.18
Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling. Proteins (2003) 3.04
DelPhi: a comprehensive suite for DelPhi software and associated resources. BMC Biophys (2012) 1.64
A catalytically silent FAAH-1 variant drives anandamide transport in neurons. Nat Neurosci (2011) 1.50
Characterizing a partially folded intermediate of the villin headpiece domain under non-denaturing conditions: contribution of His41 to the pH-dependent stability of the N-terminal subdomain. J Mol Biol (2005) 1.47
Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides. J Mol Biol (2006) 1.39
On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles. J Mol Biol (2003) 1.34
On the Dielectric "Constant" of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi. J Chem Theory Comput (2013) 1.32
Molecular mechanisms of disease-causing missense mutations. J Mol Biol (2013) 1.31
Computational analysis of missense mutations causing Snyder-Robinson syndrome. Hum Mutat (2010) 1.31
Comparative study of generalized born models: Born radii and peptide folding. J Phys Chem B (2005) 1.24
Modeling effects of human single nucleotide polymorphisms on protein-protein interactions. Biophys J (2009) 1.18
Electrostatic properties of protein-protein complexes. Biophys J (2006) 1.18
An X-linked channelopathy with cardiomegaly due to a CLIC2 mutation enhancing ryanodine receptor channel activity. Hum Mol Genet (2012) 1.16
Cancer missense mutations alter binding properties of proteins and their interaction networks. PLoS One (2013) 1.14
Homology-based modeling of 3D structures of protein-protein complexes using alignments of modified sequence profiles. Int J Biol Macromol (2008) 1.13
On the electrostatic component of protein-protein binding free energy. PMC Biophys (2008) 1.13
Predicting folding free energy changes upon single point mutations. Bioinformatics (2012) 1.12
Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies. Biophys J (2007) 1.10
In silico and in vitro investigations of the mutability of disease-causing missense mutation sites in spermine synthase. PLoS One (2011) 1.07
Analyzing effects of naturally occurring missense mutations. Comput Math Methods Med (2012) 1.04
On the role of electrostatics in protein-protein interactions. Phys Biol (2011) 1.04
PROTCOM: searchable database of protein complexes enhanced with domain-domain structures. Nucleic Acids Res (2006) 1.03
Systematic exploitation of multiple receptor conformations for virtual ligand screening. PLoS One (2011) 0.99
Electrostatic and lipid anchor contributions to the interaction of transducin with membranes: mechanistic implications for activation and translocation. J Biol Chem (2008) 0.99
JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure. Nucleic Acids Res (2004) 0.99
A missense mutation in CLIC2 associated with intellectual disability is predicted by in silico modeling to affect protein stability and dynamics. Proteins (2011) 0.99
On the pH-optimum of activity and stability of proteins. Proteins (2010) 0.98
Mapping all-atom models onto one-bead Coarse Grained Models: general properties and applications to a minimal polypeptide model. J Chem Theory Comput (2006) 0.95
Optimization of electrostatic interactions in protein-protein complexes. Biophys J (2007) 0.94
Protonation and pK changes in protein-ligand binding. Q Rev Biophys (2013) 0.94
In silico modeling of pH-optimum of protein-protein binding. Proteins (2010) 0.93
A mutation in a ganglioside biosynthetic enzyme, ST3GAL5, results in salt & pepper syndrome, a neurocutaneous disorder with altered glycolipid and glycoprotein glycosylation. Hum Mol Genet (2013) 0.93
Coating single-walled carbon nanotubes with phospholipids. J Phys Chem B (2006) 0.92
Predicting 3D structures of transient protein-protein complexes by homology. Biochim Biophys Acta (2006) 0.92
Highly efficient and exact method for parallelization of grid-based algorithms and its implementation in DelPhi. J Comput Chem (2012) 0.91
Predicting nonspecific ion binding using DelPhi. Biophys J (2012) 0.91
A Y328C missense mutation in spermine synthase causes a mild form of Snyder-Robinson syndrome. Hum Mol Genet (2013) 0.91
Steered molecular dynamics simulations for studying protein-ligand interaction in cyclin-dependent kinase 5. J Chem Inf Model (2014) 0.89
Structural and functional consequences of single amino acid substitutions in the pyrimidine base binding pocket of Escherichia coli CMP kinase. FEBS J (2007) 0.89
A general and robust ray-casting-based algorithm for triangulating surfaces at the nanoscale. PLoS One (2013) 0.88
Green fluorescent protein ground states: the influence of a second protonation site near the chromophore. Biochemistry (2007) 0.87
DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol. Bioinformatics (2012) 0.86
Sharpen&Bend: recovering curved sharp edges in triangle meshes produced by feature-insensitive sampling. IEEE Trans Vis Comput Graph (2005) 0.84
Progress in developing Poisson-Boltzmann equation solvers. Mol Based Math Biol (2013) 0.84
Developing hybrid approaches to predict pKa values of ionizable groups. Proteins (2011) 0.84
GPU linear and non-linear Poisson-Boltzmann solver module for DelPhi. Bioinformatics (2013) 0.83
Protein-protein interactions. Curr Pharm Biotechnol (2008) 0.83
The role of protonation states in ligand-receptor recognition and binding. Curr Pharm Des (2013) 0.83
Continuous development of schemes for parallel computing of the electrostatics in biological systems: implementation in DelPhi. J Comput Chem (2013) 0.82
Enhancing human spermine synthase activity by engineered mutations. PLoS Comput Biol (2013) 0.82
Application of conformational clustering in protein-ligand docking. Methods Mol Biol (2012) 0.80
BION web server: predicting non-specifically bound surface ions. Bioinformatics (2013) 0.80
Structural assessment of the effects of amino acid substitutions on protein stability and protein protein interaction. Int J Comput Biol Drug Des (2011) 0.79
Insights into Ligand-Protein Binding from Local Mechanical Response. J Chem Theory Comput (2011) 0.78
Assessing the quality of the homology-modeled 3D structures from electrostatic standpoint: test on bacterial nucleoside monophosphate kinase families. J Bioinform Comput Biol (2007) 0.78
Complexes of HIV-1 integrase with HAT proteins: multiscale models, dynamics, and hypotheses on allosteric sites of inhibition. Proteins (2009) 0.78
A rational free energy-based approach to understanding and targeting disease-causing missense mutations. J Am Med Inform Assoc (2013) 0.77
Protein Nano-Object Integrator (ProNOI) for generating atomic style objects for molecular modeling. BMC Struct Biol (2012) 0.77
Protein structure analysis online. Curr Protoc Protein Sci (2007) 0.77
A minimal contouring approach to the computation of the Reeb graph. IEEE Trans Vis Comput Graph (2009) 0.77
Predicting interacting and interfacial residues using continuous sequence segments. Int J Biol Macromol (2007) 0.76
AClAP, Autonomous hierarchical agglomerative Cluster Analysis based protocol to partition conformational datasets. Bioinformatics (2006) 0.76
Structural shape prototypes for the automatic classification of 3D objects. IEEE Comput Graph Appl (2007) 0.75
Import Vector Domain Description: A Kernel Logistic One-Class Learning Algorithm. IEEE Trans Neural Netw Learn Syst (2016) 0.75
Shape 4.0: 3D Shape Modeling and Processing Using Semantics. IEEE Comput Graph Appl (2016) 0.75
Corrigendum: Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations. Sci Rep (2016) 0.75
PypKa: a flexible Python module for Poisson-Boltzmann based p calculations. J Chem Inf Model (2020) 0.75
Probing Hydration Patterns in Class-A GPCRs via Biased MD: The A2A Receptor. J Chem Theory Comput (2016) 0.75
BANMOKI: a searchable database of homology-based 3D models and their electrostatic properties of five bacterial nucleoside monophosphate kinase families. Int J Biol Macromol (2007) 0.75