Solvent dramatically affects protein structure refinement. (Q30373863)

17 August 2017

Solvent dramatically affects protein structure refinement. (English)

1 reference

17 August 2017

0 references

3

Michael Levitt

1 reference

17 August 2017

Gaurav Chopra

1

0 references

author name string

Christopher M Summa

series ordinal

2

1 reference

PMCID

2600579

17 August 2017

language of work or name

English

0 references

publication date

10 December 2008

1 reference

17 August 2017

6

1 reference

Proceedings of the National Academy of Sciences of the United States of America

inferred from page(s)

published in

1 reference

17 August 2017

105

1 reference

17 August 2017

51

1 reference

17 August 2017

20239-20244

1 reference

Structural biology. Protein structure initiative: phase 3 or phase out.

17 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600579

Can molecular dynamics simulations provide high-resolution refinement of protein structure?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600579

Growth of novel protein structural data.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600579

Near-native structure refinement using in vacuo energy minimization.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600579

20 June 2018

Implicit solvent models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600579

Water structure of a hydrophobic protein at atomic resolution: Pentagon rings of water molecules in crystals of crambin

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600579

Physically realistic homology models built with ROSETTA can be more accurate than their templates

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600579

The impact of structural genomics: expectations and outcomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600579

GROMACS: fast, flexible, and free

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600579

Progress over the first decade of CASP experiments.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600579

Assessment of predictions submitted for the CASP6 comparative modeling category

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600579

The limit of accuracy of protein modeling: influence of crystal packing on protein structure.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600579

The protein structure prediction problem could be solved using the current PDB library

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600579

Homology-based modelling of targets for rational drug design

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600579

The state of the Protein Structure Initiative.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600579

Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600579

Refinement of homology-based protein structures by molecular dynamics simulation techniques

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600579

LGA: A method for finding 3D similarities 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=2600579

All-Atom Structure Prediction and Folding Simulations of a Stable Protein

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600579

Increasing the precision of comparative models with YASARA NOVA-a self-parameterizing 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=2600579

Implicit Solvation Models: Equilibria, Structure, Spectra, and 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=2600579

Molecular dynamics in the endgame of protein structure 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=2600579

Protein structure prediction and structural genomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600579

2.1 and 1.8 A average C(alpha) RMSD structure predictions on two small proteins, HP-36 and s15.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600579

Processing and analysis of CASP3 protein structure predictions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600579

The interpretation of protein structures: Estimation of static accessibility

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600579

Energy refinement of hen egg-white lysozyme

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600579

Accurate simulation of protein dynamics in solution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600579

Assessment of progress over the CASP experiments

20 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0810818105

GROMACS: A message-passing parallel molecular dynamics implementation

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0810818105

A discussion of the solution for the best rotation to relate two sets of vectors

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0810818105

Semianalytical treatment of solvation for molecular mechanics and dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0810818105

GROMACS 3.0: a package for molecular simulation and trajectory analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0810818105

On the limited memory BFGS method for large scale optimization

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0810818105

An X-ray study of horse methaemoglobin

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600579

A critical analysis of continuum electrostatics: the screened Coulomb potential--implicit solvent model and the study of the alanine dipeptide and discrimination of misfolded structures of proteins

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2600579

Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19073921

12 December 2020

inferred from PubMed ID database lookup

X-ray studies of water in crystals of lysozyme

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19073921

12 December 2020

inferred from PubMed ID database lookup

Refinement of protein conformations using a macromolecular energy minimization procedure

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19073921

12 December 2020

inferred from PubMed ID database lookup

Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1073/PNAS.0810818105

Identifiers

DOI

10.1073/PNAS.0810818105

1 reference

17 August 2017

0 references

1 reference

17 August 2017

1 reference

PMCID

2600579