TOUCHSTONE II: a new approach to ab initio protein structure prediction (Q30333234)

18 September 2017

TOUCHSTONE II: a new approach to ab initio protein structure prediction (English)

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protein structure prediction

18 September 2017

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3

Jeffrey Skolnick

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18 September 2017

Andrzej Kolinski

2

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Yang Zhang

object named as

Yang Zhang

series ordinal

1

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language of work or name

English

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publication date

1 August 2003

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18 September 2017

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18 September 2017

85

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18 September 2017

1145-1164

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18 September 2017

2

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TOUCHSTONEX: protein structure prediction with sparse NMR data.

18 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303233

Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303233

TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303233

Stretching single-stranded DNA: interplay of electrostatic, base-pairing, and base-pair stacking interactions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303233

Generalized comparative modeling (GENECOMP): a combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303233

From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303233

Prospects for ab initio protein structural genomics.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303233

Recent improvements in prediction of protein structure by global optimization of a potential energy function.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303233

Defrosting the frozen approximation: PROSPECTOR--a new approach to threading.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303233

A surprising simplicity to protein folding.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303233

3 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=1303233

Protein secondary structure prediction based on position-specific scoring matrices

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303233

Hidden Markov models for detecting remote protein homologies

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303233

Clustering of low-energy conformations near the native structures of small proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303233

Assembly of protein structure from sparse experimental data: an efficient Monte Carlo model

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303233

SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303233

Evaluation of comparative protein structure modeling by MODELLER-3.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303233

Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303233

Combining evolutionary information and neural networks to predict protein secondary structure

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303233

A simple method for displaying the hydropathic character of a protein

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303233

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303233

Prediction of protein antigenic determinants from amino acid sequences

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303233

Principles that govern the folding of protein chains

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303233

Patterns of divergence in homologous proteins as indicators of secondary and tertiary structure: a prediction of the structure of the catalytic domain of protein kinases

3 June 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303233

3 June 2018

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974551-2

A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional Structure

7 January 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303233

Combination of threading potentials and sequence profiles improves fold recognition.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303233

Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading?

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303233

Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303233

Progress in protein structure prediction

26 November 2018

1 reference

Crossref

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974551-2

Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins

7 January 2021

2 references

Crossref

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974551-2

7 January 2021

https://pubmed.ncbi.nlm.nih.gov/12885659

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Distance-dependent, pair potential for protein folding: results from linear optimization

1 reference

Crossref

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974551-2

10.1016/S0006-3495(03)74551-2

7 January 2021

Identifiers

DOI

1 reference

18 September 2017

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18 September 2017

1 reference

PMCID

1303233