(Q35218259)

7 August 2017

title

Automated real-space refinement of protein structures using a realistic backbone move set. (English)

1 reference

7 August 2017

0 references

8

Tobin R Sosnick

1 reference

7 August 2017

9

Karl F Freed

1 reference

7 August 2017

Esmael J Haddadian

1

1 reference

7 August 2017

Haipeng Gong

2

1 reference

7 August 2017

Abhishek K Jha

3

1 reference

7 August 2017

Xiaojing Yang

4

1 reference

7 August 2017

Joe Debartolo

5

1 reference

7 August 2017

James R Hinshaw

6

1 reference

7 August 2017

Phoebe A Rice

7

1 reference

7 August 2017

language of work or name

English

0 references

publication date

1 August 2011

1 reference

7 August 2017

1 reference

7 August 2017

volume

101

1 reference

7 August 2017

issue

4

1 reference

7 August 2017

page(s)

899-909

1 reference

REFMAC5 for the refinement of macromolecular crystal structures

7 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

The 2.5 Å structure of CD1c in complex with a mycobacterial lipid reveals an open groove ideally suited for diverse antigen presentation

13 July 2018

1 reference

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Structural basis for the unfolding of anthrax lethal factor by protective antigen oligomers

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

Consistent refinement of submitted models at CASP using a knowledge-based potential

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

Neighbor-dependent Ramachandran probability distributions of amino acids developed from a hierarchical Dirichlet process model

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

Features and development of Coot

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

Super-resolution biomolecular crystallography with low-resolution data

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

Reduced C(beta) statistical potentials can outperform all-atom potentials in decoy identification

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

TAP score: torsion angle propensity normalization applied to local protein structure evaluation.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

Near-native structure refinement using in vacuo energy minimization.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

Minimalist representations and the importance of nearest neighbor effects in protein folding simulations

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

A method for evaluating the structural quality of protein models by using higher-order phi-psi pairs scoring

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

Shaping up the protein folding funnel by local interaction: lesson from a structure prediction study

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

Progress over the first decade of CASP experiments.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

Toward high-resolution de novo structure prediction for small proteins.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

Statistical coil model of the unfolded state: resolving the reconciliation problem

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

PISCES: recent improvements to a PDB sequence culling server

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

Discrete restraint-based protein modeling and the Calpha-trace problem

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

Structure validation by Calpha geometry: phi,psi and Cbeta deviation

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

PHENIX: building new software for automated crystallographic structure determination

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

The Flory isolated-pair hypothesis is not valid for polypeptide chains: implications for protein folding

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

Efficient anisotropic refinement of macromolecular structures using FFT

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

VMD: visual molecular dynamics

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

Conformation of Polypeptides and Proteins

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

Crystallographic refinement by knowledge-based exploration of complex energy landscapes.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

Relationships between amino acid sequence and backbone torsion angle preferences.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the Flory isolated-pair hypothesis for peptides

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175057

Local propensities and statistical potentials of backbone dihedral angles in proteins

26 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21843481

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Polypeptide motions are dominated by peptide group oscillations resulting from dihedral angle correlations between nearest neighbors

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21843481

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.BPJ.2011.06.063

1 reference

7 August 2017

1 reference

7 August 2017

1 reference