DelPhi: a comprehensive suite for DelPhi software and associated resources (Q21195848)

2

Chuan

Li

1 reference

18 August 2022

Subhra Sarkar

3

Subhra

Sarkar

1 reference

18 August 2022

Jie Zhang

4

Jie

Zhang

1 reference

18 August 2022

Shawn Witham

5

Shawn

Witham

1 reference

18 August 2022

Zhe Zhang

6

Zhe

Zhang

1 reference

18 August 2022

Lin Wang

7

Lin

Wang

1 reference

18 August 2022

Nicholas Smith

8

Nicholas

Smith

1 reference

18 August 2022

Marharyta Petukh

9

Marharyta

Petukh

1 reference

18 August 2022

Emil Alexov

10

Emil

Alexov

1 reference

https://scigraph.springernature.com/pub.10.1186/2046-1682-5-9

18 August 2022

language of work or name

English

0 references

publication date

2012

0 references

published in

BMC Biophysics

0 references

volume

5

0 references

page(s)

9

0 references

issue

1

0 references

exact match

0 references

cites work

CHARMM: the biomolecular simulation program

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

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

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

TM-align: a protein structure alignment algorithm based on the TM-score

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

UCSF Chimera--a visualization system for exploratory research and analysis

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

VMD: visual molecular dynamics

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

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

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

In silico and in vitro investigations of the mutability of disease-causing missense mutation sites in spermine synthase

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

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

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

Classical electrostatics in biology and chemistry

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

Using DelPhi capabilities to mimic protein's conformational reorganization with amino acid specific dielectric constants

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

Three force fields' views of the 3(10) helix.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

Developing hybrid approaches to predict pKa values of ionizable groups

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

A missense mutation in CLIC2 associated with intellectual disability is predicted by in silico modeling to affect protein stability and dynamics

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

On the role of electrostatics in protein-protein interactions

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

Computational analysis of missense mutations causing Snyder-Robinson syndrome

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

Secondary structure propensities in peptide folding simulations: a systematic comparison of molecular mechanics interaction schemes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

Calculating pH and salt dependence of protein-protein binding

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

Biskit--a software platform for structural bioinformatics

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

Force fields for protein simulations

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

Explicit and implicit water simulations of a beta-hairpin peptide

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

Treatment of electrostatic effects in macromolecular modeling

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

Electrostatic interactions in macromolecules: theory and applications

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

On the electrostatic component of protein-protein binding free energy

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

An improved OPLS-AA force field for carbohydrates

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

On the calculation of electrostatic interactions in proteins.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

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

30 May 2018

1 reference

https://api.crossref.org/works/10.1186%2F2046-1682-5-9

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F2046-1682-5-9

On the pH dependence of protein stability.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F2046-1682-5-9

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F2046-1682-5-9

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F2046-1682-5-9

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F2046-1682-5-9

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F2046-1682-5-9

Highly accurate biomolecular electrostatics in continuum dielectric environments.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F2046-1682-5-9

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F2046-1682-5-9

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

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

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

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

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

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3463482

Protein-water electrostatics and principles of bioenergetics

29 November 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

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

Identifiers

DOI

10.1186/2046-1682-5-9

1 reference

1141868

0 references

1141868

1 reference

1 reference

1 reference