(Q42585482)

3 November 2017

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

1 reference

3 November 2017

3

1 reference

3 November 2017

Matthew P Jacobson

5

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author name string

Benjamin D Sellers

series ordinal

1

1 reference

3 November 2017

Kai Zhu

series ordinal

2

1 reference

3 November 2017

Richard A Friesner

series ordinal

4

1 reference

3 November 2017

language of work or name

English

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publication date

1 August 2008

1 reference

3 November 2017

1 reference

3 November 2017

72

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3 November 2017

3

1 reference

3 November 2017

959-971

1 reference

Ensemble Refinement of Protein Crystal Structures: Validation and Application

3 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764870

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764870

Conformational changes in protein loops and helices induced by post-translational phosphorylation

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764870

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764870

Novel human lipoxygenase inhibitors discovered using virtual screening with homology models

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764870

Protein loop structure prediction with flexible stem geometries.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764870

Assessment of predictions submitted for the CASP6 comparative modeling category

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764870

Critical assessment of methods of protein structure prediction (CASP)--round 6.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764870

A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764870

Progress and challenges in high-resolution refinement of protein structure models.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764870

Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764870

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764870

A hierarchical approach to all-atom protein loop prediction

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764870

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764870

Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water?

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764870

Protein structure prediction and structural genomics

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764870

Extending the accuracy limits of prediction for side-chain conformations

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764870

CODA: a combined algorithm for predicting the structurally variable regions of protein models.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764870

Modeling of loops in protein structures

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764870

Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764870

PDB-based protein loop prediction: parameters for selection and methods for optimization.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764870

An algorithm for determining the conformation of polypeptide segments in proteins by systematic search

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764870

Basic local alignment search tool

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764870

Long loop prediction using the protein local optimization program

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764870

The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764870

Completeness in structural genomics

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2764870

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

16 August 2018

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

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

1 reference

12 December 2020

Prediction of the folding of short polypeptide segments by uniform conformational sampling

1 reference

12 December 2020

Identifiers

DOI

10.1002/PROT.21990

1 reference

release_ibthjvz5evgppevahximerodla

3 November 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/ibthjvz5evgppevahximerodla

24 November 2022

mapped directly with Wikidata item

1 reference

3 November 2017

PubMed publication ID

18300241

1 reference