DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes (Q37664910)

21 August 2017

DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes (English)

1 reference

21 August 2017

DelPhi Web Server: A Comprehensive Online Suite for Electrostatic Calculations of Biological Macromolecules and Their Complexes (English)

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1 reference

1 reference

Subhra Sarkar

1 reference

21 August 2017

Shawn Witham

1 reference

21 August 2017

Jie Zhang

1 reference

21 August 2017

Maxim Zhenirovskyy

1 reference

21 August 2017

Walter Rocchia

1 reference

21 August 2017

Emil Alexov

1 reference

21 August 2017

1 January 2013

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Communications in Computational Physics

21 August 2017

January 2013

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published in

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21 August 2017

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21 August 2017

1 reference

21 August 2017

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page(s)

269-284

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maintained by WikiProject

21 August 2017

WikiProject Mathematics

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cites work

PAComplex: a web server to infer peptide antigen families and binding models from TCR-pMHC complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

On the role of electrostatics in protein-protein interactions

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Web servers and services for electrostatics calculations with APBS and PDB2PQR

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

PUDGE: a flexible, interactive server for protein structure prediction

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

I-TASSER: a unified platform for automated protein structure and function prediction

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

I-TASSER: fully automated protein structure prediction in CASP8

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

CHARMM: the biomolecular simulation program

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

PSI-BLAST pseudocounts and the minimum description length principle.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

PBEQ-Solver for online visualization of electrostatic potential of biomolecules

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Calculating pH and salt dependence of protein-protein binding

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Continuum molecular electrostatics, salt effects, and counterion binding--a review of the Poisson-Boltzmann theory and its modifications

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Explicit-solvent molecular dynamics simulations of the polysaccharide schizophyllan in water

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Adding explicit solvent molecules to continuum solvent calculations for the calculation of aqueous acid dissociation constants

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

The RCSB PDB information portal for structural genomics

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Comparison between Generalized-Born and Poisson-Boltzmann methods in physics-based scoring functions for protein structure prediction.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

The FoldX web server: an online force field

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

PCE: web tools to compute protein continuum electrostatics

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Force fields for protein simulations

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Free energy landscape of protein folding in water: Explicit vs. implicit solvent

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

SAWTED: structure assignment with text description--enhanced detection of remote homologues with automated SWISS-PROT annotation comparisons.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Explicit and implicit water simulations of a beta-hairpin peptide

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Iterated profile searches with PSI-BLAST--a tool for discovery in protein databases

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Discrepancies between the NMR and X-ray structures of uncomplexed barstar: analysis suggests that packing densities of protein structures determined by NMR are unreliable

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

(-)-3 beta-Substituted ecgonine methyl esters as inhibitors for cocaine binding and dopamine uptake

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Classical electrostatics in biology and chemistry

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Calculation of electrostatic effects at the amino terminus of an alpha helix

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

In silico modeling of pH-optimum of protein-protein binding

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Explicit-water molecular dynamics study of a short-chain 3,3 ionene in solutions with sodium halides

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Treatment of electrostatic effects in macromolecular modeling

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Electrostatic interactions in macromolecules: theory and applications

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

webPIPSA: a web server for the comparison of protein interaction properties

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Biomolecular electrostatics with the linearized Poisson-Boltzmann equation

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

MIBPB: A software package for electrostatic analysis

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

HexServer: an FFT-based protein docking server powered by graphics processors.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

An improved OPLS-AA force field for carbohydrates

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

On the calculation of electrostatic interactions in proteins.

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

A performance enhanced PSI-BLAST based on hybrid alignment

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Electrostatics in the stability and misfolding of the prion protein: salt bridges, self energy, and solvation

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Trypano-PPI: a web server for prediction of unique targets in trypanosome proteome by using electrostatic parameters of protein-protein interactions.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Implicit and explicit solvent models for the simulation of a single polymer chain in solution: Lattice Boltzmann versus Brownian dynamics.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

SIB-BLAST: a web server for improved delineation of true and false positives in PSI-BLAST searches

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

A hybrid explicit/implicit solvation method for first-principle molecular dynamics simulations

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Treatment of charge singularities in implicit solvent models.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Patch Finder Plus (PFplus): a web server for extracting and displaying positive electrostatic patches on protein surfaces

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

How well does Poisson-Boltzmann implicit solvent agree with explicit solvent? A quantitative analysis

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Effects of pH, salt, and macromolecular crowding on the stability of FK506-binding protein: an integrated experimental and theoretical study

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Numerical calculations of the pH of maximal protein stability. The effect of the sequence composition and three-dimensional structure

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Parameterization of OPLS-AA force field for the conformational analysis of macrocyclic polyketides

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Role of main-chain electrostatics, hydrophobic effect and side-chain conformational entropy in determining the secondary structure of proteins

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

On the pH dependence of protein stability.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Correlating solvation free energies and surface tensions of hydrocarbon solutes.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Calculations of electrostatic energies in proteins. The energetics of ionized groups in bovine pancreatic trypsin inhibitor

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Implicit versus explicit solvent in free energy calculations of enzyme catalysis: Methyl transfer catalyzed by catechol O-methyltransferase

2 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3966485

Protein-water electrostatics and principles of bioenergetics

3 December 2018

1 reference

12 December 2020

Poisson–Boltzmann Methods for Biomolecular Electrostatics

1 reference

12 December 2020

On the calculation of pKas in proteins

1 reference

12 December 2020

A comparison of implicit- and explicit-solvent simulations of self-assembly in block copolymer and solute systems

1 reference

12 December 2020

Calculation of the electric potential in the active site cleft due to alpha-helix dipoles

1 reference

12 December 2020

Modifying the OPLS-AA force field to improve hydration free energies for several amino acid side chains using new atomic charges and an off-plane charge model for aromatic residues

1 reference

12 December 2020

Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling

1 reference

12 December 2020

10.4208/CICP.300611.201011S

Identifiers

DOI

0 references

1 reference

21 August 2017

PubMed publication ID

24683424

1 reference