(Q34612025)

3 August 2017

title

Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. (English)

1 reference

3 August 2017

David Baker

8

0 references

author name string

Elmar Krieger

1

1 reference

3 August 2017

Keehyoung Joo

2

1 reference

3 August 2017

Jinwoo Lee

3

1 reference

3 August 2017

Jooyoung Lee

4

1 reference

3 August 2017

Srivatsan Raman

5

1 reference

3 August 2017

James Thompson

6

1 reference

3 August 2017

Mike Tyka

7

1 reference

3 August 2017

Kevin Karplus

9

1 reference

3 August 2017

language of work or name

English

0 references

publication date

1 January 2009

1 reference

3 August 2017

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3 August 2017

volume

77 Suppl 9

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3 August 2017

page(s)

114-122

1 reference

All-atom empirical potential for molecular modeling and dynamics studies of proteins

3 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=2922016

The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2922016

Applying undertaker cost functions to model quality assessment.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2922016

Multiple sequence alignment by conformational space annealing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2922016

High accuracy template based modeling by global optimization

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2922016

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2922016

The backrub motion: how protein backbone shrugs when a sidechain dances

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2922016

The fumarate sensor DcuS: progress in rapid protein fold elucidation by combining protein structure prediction methods with NMR spectroscopy.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2922016

Making optimal use of empirical energy functions: force-field parameterization in crystal space

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2922016

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2922016

A graph-theory algorithm for rapid protein side-chain prediction

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2922016

Cyclic coordinate descent: A robotics algorithm for protein loop closure.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2922016

Stochastic pairwise alignments

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2922016

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2922016

Increasing the precision of comparative models with YASARA NOVA-a self-parameterizing force field

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2922016

Models@Home: distributed computing in bioinformatics using a screensaver based approach

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2922016

Global optimization of clusters, crystals, and biomolecules.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2922016

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2922016

Errors in protein structures

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2922016

Comparative protein modelling by satisfaction of spatial restraints

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2922016

SSALN: an alignment algorithm using structure-dependent substitution matrices and gap penalties learned from structurally aligned protein pairs.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2922016

DRESS: a database of REfined solution NMR structures.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2922016

Prediction of protein conformational freedom from distance constraints

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2922016

Improvements and Extensions in the Conformational Database Potential for the Refinement of NMR and X-ray Structures of Proteins and Nucleic Acids

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2922016

Unbiased global optimization of Lennard-Jones clusters for N < or =201 using the conformational space annealing method

9 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19768677

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

All-atom chain-building by optimizing MODELLER energy function using conformational space annealing

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19768677

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PROT.22570

1 reference

3 August 2017

1 reference

3 August 2017

1 reference