Loop modeling: Sampling, filtering, and scoring (Q41875634)

13 October 2017

Loop modeling: Sampling, filtering, and scoring (English)

1 reference

13 October 2017

Lucy Forrest

4

0 references

author name string

Cinque S Soto

1

1 reference

13 October 2017

Marc Fasnacht

2

1 reference

13 October 2017

Jiang Zhu

3

1 reference

13 October 2017

Barry Honig

5

1 reference

13 October 2017

language of work or name

English

0 references

publication date

1 February 2008

1 reference

13 October 2017

1 reference

13 October 2017

70

1 reference

13 October 2017

834-843

1 reference

13 October 2017

3

1 reference

Structural refinement of protein segments containing secondary structure elements: Local sampling, knowledge-based potentials, and clustering

13 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553011

Protein structure prediction: inroads to biology.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553011

Modeling flexible loops in the dark-adapted and activated states of rhodopsin, a prototypical G-protein-coupled receptor

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553011

Protein structure modeling in the proteomics era.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553011

Modeling structurally variable regions in homologous proteins with rosetta.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553011

Protein structure prediction using Rosetta

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553011

A hierarchical approach to all-atom protein loop prediction

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553011

Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553011

The second extracellular loop of the dopamine D2 receptor lines the binding-site crevice

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553011

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553011

The Xplor-NIH NMR molecular structure determination package

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553011

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553011

Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553011

Extending the accuracy limits of prediction for side-chain conformations

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553011

SNPs, protein structure, and disease.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553011

Modeling of loops in protein structures

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553011

5 June 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553011

An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553011

Evaluation of the conformational free energies of loops in proteins.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553011

Long loop prediction using the protein local optimization program.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553011

Loops In Proteins (LIP)--a comprehensive loop database for homology modelling.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553011

On the kinematics of protein folding.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553011

Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553011

Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553011

Importance of anchor group positioning in protein loop prediction.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553011

The role of loop 7 in mediating calcineurin regulation

18 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17729286

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Predicting antibody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structures

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17729286

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PROT.21612

1 reference

13 October 2017

1 reference

13 October 2017

1 reference