De novo prediction of polypeptide conformations using dihedral probability grid Monte Carlo methodology (Q36279222)

13 August 2017

De novo prediction of polypeptide conformations using dihedral probability grid Monte Carlo methodology (English)

1 reference

13 August 2017

J S Evans

1

1 reference

13 August 2017

A M Mathiowetz

series ordinal

2

1 reference

13 August 2017

S I Chan

series ordinal

3

1 reference

13 August 2017

W A Goddard

series ordinal

4

1 reference

13 August 2017

1 June 1995

1 reference

13 August 2017

1 reference

13 August 2017

4

1 reference

13 August 2017

6

1 reference

13 August 2017

1203-1216

1 reference

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

13 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143148

SOPM: a self-optimized method for protein secondary structure prediction

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143148

Folding of immunogenic peptide fragments of proteins in water solution. I. Sequence requirements for the formation of a reverse turn

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143148

Analysis of protein loop closure. Two types of hinges produce one motion in lactate dehydrogenase

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143148

An automated method for modeling proteins on known templates using distance geometry

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143148

Conversion from a virtual-bond chain to a complete polypeptide backbone chain.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143148

Can a simple function for the dielectric response model electrostatic effects in globular proteins?

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143148

A prediction of tertiary structures of peptide by the Monte Carlo simulated annealing method.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143148

High directional Monte Carlo procedure coupled with the temperature heating and annealing as a method to obtain the global energy minimum structure of polypeptides and proteins

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143148

Molecular modeling of proteins: a strategy for energy minimization by molecular mechanics in the AMBER force field.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143148

Electrostatic effects in proteins: comparison of dielectric and charge models

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143148

Cutoff size does strongly influence molecular dynamics results on solvated polypeptides

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143148

Extracting information on folding from the amino acid sequence: accurate predictions for protein regions with preferred conformation in the absence of tertiary interactions

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143148

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

29 June 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560040618

A method for rapidly assessing and refining simple solvent treatments in molecular modelling. Example studies on the antigen-combining loop H2 from FAB fragment McPC603.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560040618

Conformations of folded proteins in restricted spaces

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560040618

Investigation of conformational equilibrium of polypeptides by internal coordinate stochastic dynamics. Met5-enkephalin.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560040618

Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560040618

Predicting coiled coils from protein sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560040618

Capping interactions in isolated alpha helices: position-dependent substitution effects and structure of a serine-capped peptide helix

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560040618

Polyproline, beta-turn helices. Novel secondary structures proposed for the tandem repeats within rhodopsin, synaptophysin, synexin, gliadin, RNA polymerase II, hordein, and gluten

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560040618

NMR evidence for multiple conformations in a highly helical model peptide.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560040618

Equation of State Calculations by Fast Computing Machines

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560040618

Computational complexity of a problem in molecular structure prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560040618

Prediction of the native conformation of a polypeptide by a statistical-mechanical procedure. I. Backbone structure of enkephalin.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560040618

Rapid and sensitive sequence comparison with FASTP and FASTA

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560040618

UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560040618

Computer modeling and folding of four-helix bundles

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560040618

Assembly of polypeptide and protein backbone conformations from low energy ensembles of short fragments: Development of strategies and construction of models for myoglobin, lysozyme, and thymosin β4

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560040618

Simulations of the folding of a globular protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560040618

Dynamic Monte Carlo simulations of a new lattice model of globular protein folding, structure and dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560040618

An all atom force field for simulations of proteins and nucleic acids

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560040618

Beta-turns and their distortions: a proposed new nomenclature

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560040618

Characterization of radioiodinated recombinant human TGF-beta 1 binding to bone matrix within rabbit skull defects

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143148

Analysis of protein loop closure

22 September 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560040618

An evaluation of implicit and explicit solvent model systems for the molecular dynamics simulation of bacteriophage T4 lysozyme

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2143148

Comparison of lattice Monte Carlo dynamics and Brownian dynamics folding pathways of α-helical hairpins

21 October 2018

1 reference

https://api.crossref.org/works/10.1002%2FPRO.5560040618

Hamiltonians for Protein Tertiary Structure Prediction Based on Three-dimensional Environment Principles

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/7549884

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Amino acid side-chain populations in aqueous and saline solution: bis-penicillamine enkephalin

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/7549884

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Biologically active Arg-Gly-Asp oligopeptides assume a type II beta-turn in solution

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/7549884

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PRO.5560040618

1 reference

13 August 2017

1 reference

13 August 2017

PubMed publication ID

7549884

1 reference