The VSGB 2.0 model: a next generation energy model for high resolution protein structure modeling (Q30406909)

7 September 2017

The VSGB 2.0 model: a next generation energy model for high resolution protein structure modeling (English)

1 reference

7 September 2017

Suwen Zhao

5

0 references

author name string

Jianing Li

1

1 reference

7 September 2017

Robert Abel

2

1 reference

7 September 2017

Kai Zhu

3

1 reference

7 September 2017

Yixiang Cao

4

1 reference

7 September 2017

Richard A Friesner

6

1 reference

7 September 2017

language of work or name

English

0 references

publication date

22 August 2011

1 reference

7 September 2017

1 reference

7 September 2017

79

1 reference

7 September 2017

10

1 reference

7 September 2017

2794-2812

1 reference

Progress in super long loop prediction.

7 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

The AGBNP2 Implicit Solvation Model.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

Current status of the AMOEBA polarizable force field

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

Hydrogen bonding and pi-stacking: how reliable are force fields? A critical evaluation of force field descriptions of nonbonded interactions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

Recognition of a flipped base in a hairpinloop DNA by a small peptide

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

A histidine/tryptophan pi-stacking interaction stabilizes the heme-independent folding core of microsomal apocytochrome b5 relative to that of mitochondrial apocytochrome b5.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

Structure selection for protein kinase docking and virtual screening: homology models or crystal structures?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

Protein-ligand docking: current status and future challenges

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

Base-stacking and base-pairing contributions into thermal stability of the DNA double helix

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

Comparative study of generalized Born models: protein dynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

A hierarchical approach to all-atom protein loop prediction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

Virtual screening for kinase targets

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

Improved protein-ligand docking using GOLD

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

SWISS-MODEL: An automated protein homology-modeling server

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

A possible role for pi-stacking in the self-assembly of amyloid fibrils

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

Extending the accuracy limits of prediction for side-chain conformations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

Ab initio modeling of small, medium, and large loops in proteins.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

Modeling of loops in protein structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

Theory of protein folding: the energy landscape perspective

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

What function for human lithostathine?: structural investigations by three-dimensional structure modeling and high-resolution NMR spectroscopy

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

Comparative protein modelling by satisfaction of spatial restraints

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

Do salt bridges stabilize proteins? A continuum electrostatic analysis.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

Funnels, pathways, and the energy landscape of protein folding: a synthesis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

Aromatic-aromatic interaction: a mechanism of protein structure stabilization

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

Database of homology-derived protein structures and the structural meaning of sequence alignment

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3206729

Accurate First Principles Calculation of Molecular Charge Distributions and Solvation Energies from Ab Initio Quantum Mechanics and Continuum Dielectric Theory

20 June 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23106

AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23106

Long loop prediction using the protein local optimization program.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23106

Improved Methods for Side Chain and Loop Predictions via the Protein Local Optimization Program: Variable Dielectric Model for Implicitly Improving the Treatment of Polarization Effects.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23106

Generalized born model with a simple smoothing function.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23106

Investigation of Salt Bridge Stability in a Generalized Born Solvent Model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23106

Toward better refinement of comparative models: predicting loops in inexact environments

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23106

Semianalytical treatment of solvation for molecular mechanics and dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23106

Effects of the biological backbone on DNA-protein stacking interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23106

Stacking and T-shape competition in aromatic-aromatic amino acid interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23106

Self-contacts in Asx and Glx residues of high-resolution protein structures: role of local environment and tertiary interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23106

Influence of protonation, tautomeric, and stereoisomeric states on protein-ligand docking results

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23106

Constant-pH molecular dynamics with ionic strength effects: protonation-conformation coupling in decalysine.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23106

Force Field Validation Using Protein Side Chain Prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23106

On the Role of the Crystal Environment in Determining Protein Side-chain Conformations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23106

Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23106

Contribution of unusual arginine-arginine short-range interactions to stabilization and recognition in proteins

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21905107

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Structure-based drug discovery using GPCR homology modeling: successful virtual screening for antagonists of the alpha1A adrenergic receptor

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21905107

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PROT.23106

1 reference

release_edgwrpgq75axbjnjexj7q7wuky

7 September 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/edgwrpgq75axbjnjexj7q7wuky

mapped directly with Wikidata item

24 November 2022

based on heuristic

1 reference

7 September 2017

1 reference