(Q42109476)

16 October 2017

Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling (English)

1 reference

16 October 2017

0 references

Yelena A Arnautova

1

1 reference

16 October 2017

Ruben A Abagyan

series ordinal

2

1 reference

16 October 2017

Maxim Totrov

series ordinal

3

1 reference

16 October 2017

language of work or name

English

0 references

publication date

1 February 2011

1 reference

16 October 2017

1 reference

16 October 2017

79

1 reference

16 October 2017

2

1 reference

16 October 2017

477-498

1 reference

New computational method for prediction of interacting protein loop regions.

16 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

Backbone statistical potential from local sequence-structure interactions in protein loops

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

Conformation dependence of backbone geometry in proteins.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

Loop modeling: Sampling, filtering, and scoring

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

A new force field (ECEPP-05) for peptides, proteins, and organic molecules

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

Coupling between conformation and proton binding in proteins.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

Modeling structurally variable regions in homologous proteins with rosetta.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

A hierarchical approach to all-atom protein loop prediction

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

Solvation parameters for predicting the structure of surface loops in proteins: Transferability and entropic effects

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

Conformation-family Monte Carlo: a new method for crystal structure prediction

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

High-throughput docking for lead generation

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

Ab initio modeling of small, medium, and large loops in proteins.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

Modeling of loops in protein structures

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

The penultimate rotamer library

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

29 May 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=3057902

Flexible protein-ligand docking by global energy optimization in internal coordinates.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

Experimentally observed conformation-dependent geometry and hidden strain in proteins

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

Homology modeling by the ICM method

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

Conformations of immunoglobulin hypervariable regions

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

Evaluation of the conformational free energies of loops in proteins.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

Ramachandran revisited. DFT energy surfaces of diastereomeric trialanine peptides in the gas phase and aqueous solution

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

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

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

Long loop prediction using the protein local optimization program.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

Application of torsion angle molecular dynamics for efficient sampling of protein conformations

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

Folding of the villin headpiece subdomain from random structures. Analysis of the charge distribution as a function of pH.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

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

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

Improved treatment of the protein backbone in empirical force fields.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

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

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

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

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

Optimization of solvation models for predicting the structure of surface loops in proteins

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057902

Force Field Influence on the Observation of π-Helical Protein Structures in Molecular Dynamics Simulations

3 November 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPROT.22896

On the influence of thermal motion on the crystal structures and polymorphism of even n-alkanes

21 January 2018

1 reference

12 December 2020

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

1 reference

12 December 2020

On the irrelevance of electrostatics for the crystal structures and polymorphism of long even n-alkanes

1 reference

12 December 2020

Homology modeling with internal coordinate mechanics: deformation zone mapping and improvements of models via conformational search

1 reference

12 December 2020

Canonical structures for the hypervariable regions of immunoglobulins

1 reference

12 December 2020

Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions

1 reference

12 December 2020

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

1 reference

12 December 2020

Prediction of loop geometries using a generalized born model of solvation effects

1 reference

12 December 2020

Systematic analysis of structural data as a research technique in organic chemistry

1 reference

COCI

https://opencitations.net/index/coci/api/v1/citations/10.1021/AR00089A001

5 March 2023

Identifiers

DOI

10.1002/PROT.22896

1 reference

release_kd3qrqtbrndl3arliitvot2une

16 October 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/kd3qrqtbrndl3arliitvot2une

24 November 2022

mapped directly with Wikidata item

1 reference

16 October 2017

PubMed publication ID

21069716

1 reference