(Q36281436)

English

Sequence specificity, statistical potentials, and three-dimensional structure prediction with self-correcting distance geometry calculations of beta-sheet formation in proteins

scientific article

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scholarly article

1 reference

Europe PubMed Central

13 August 2017

Sequence specificity, statistical potentials, and three-dimensional structure prediction with self-correcting distance geometry calculations of beta-sheet formation in proteins (English)

1 reference

Europe PubMed Central

13 August 2017

0 references

protein structure prediction

0 references

protein structure

0 references

author name string

Zhu H

1

1 reference

Europe PubMed Central

13 August 2017

Braun W

2

1 reference

Europe PubMed Central

13 August 2017

publication date

1 February 1999

1 reference

Europe PubMed Central

13 August 2017

Protein Science

1 reference

Europe PubMed Central

13 August 2017

8

1 reference

Europe PubMed Central

13 August 2017

326-342

1 reference

Europe PubMed Central

13 August 2017

2

1 reference

Europe PubMed Central

13 August 2017

De novo protein design: fully automated sequence selection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

30 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

30 September 2017

How to derive a protein folding potential? A new approach to an old problem

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

30 September 2017

The disulphide beta-cross: from cystine geometry and clustering to classification of small disulphide-rich protein folds

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

30 September 2017

A 2.2 A resolution crystal structure of a designed zinc finger protein bound to DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

30 September 2017

Energy functions that discriminate X-ray and near native folds from well-constructed decoys

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

30 September 2017

The roles of partly folded intermediates in protein folding.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

30 September 2017

Why are the same protein folds used to perform different functions?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

30 September 2017

An empirical energy function for threading protein sequence through the folding motif

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

30 September 2017

Identification and classification of protein fold families

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

30 September 2017

Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

30 September 2017

De novo design of beta-sheet proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

30 September 2017

SCOP: a structural classification of proteins database for the investigation of sequences and structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

30 September 2017

Knowledge-based potentials for proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

30 September 2017

Free energy determinants of secondary structure formation: II. Antiparallel beta-sheets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

30 September 2017

Correlations between internal mobility and stability of globular proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

30 September 2017

The anatomy and taxonomy of protein structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

30 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

30 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

30 September 2017

Protein folding and protein refolding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

30 September 2017

Topology fingerprint approach to the inverse protein folding problem

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

30 September 2017

Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

30 September 2017

The Protein Data Bank. A computer-based archival file for macromolecular structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

30 September 2017

Empirical Predictions of Protein Conformation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

30 September 2017

Protein design: the choice of de novo sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

30 September 2017

Pattern recognition and self-correcting distance geometry calculations applied to myohemerythrin.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

29 June 2018

A thermodynamic scale for the beta-sheet forming tendencies of the amino acids.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

29 June 2018

Predicting the helix packing of globular proteins by self-correcting distance geometry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

29 June 2018

An analysis of side chain interactions and pair correlations within antiparallel beta-sheets: the differences between backbone hydrogen-bonded and non-hydrogen-bonded residue pairs.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

29 June 2018

Secondary structure predictions and medium range interactions.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

29 June 2018

Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

29 June 2018

Contact potential that recognizes the correct folding of globular proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

29 June 2018

Conformational preferences of amino acids in globular proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

29 June 2018

Search for the most stable folds of protein chains: II. Computation of stable architectures of beta-proteins using a self-consistent molecular field theory.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

22 September 2018

Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

22 September 2018

Thermodynamic beta-sheet propensities measured using a zinc-finger host peptide.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

22 September 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

22 September 2018

Phi-psi conformational pattern clustering of protein amino acid residues using the potential function method.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

22 September 2018

Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: comparison with experimental scales.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

22 September 2018

Extensive distance geometry calculations with different NOE calibrations: new criteria for structure selection applied to Sandostatin and BPTI.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2144259

22 September 2018

Measurement of the β-sheet-forming propensities of amino acids

1 reference

https://pubmed.ncbi.nlm.nih.gov/10048326

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Context is a major determinant of β-sheet propensity

1 reference

https://pubmed.ncbi.nlm.nih.gov/10048326

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Side-Chain Determinants of .beta.-Sheet Stability

1 reference

https://pubmed.ncbi.nlm.nih.gov/10048326

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Guidelines for protein design: the energetics of beta sheet side chain interactions

1 reference

https://pubmed.ncbi.nlm.nih.gov/10048326

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Why do protein architectures have Boltzmann-like statistics?

1 reference

https://pubmed.ncbi.nlm.nih.gov/10048326

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Specific recognition in the tertiary structure of beta-sheets of proteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/10048326

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The frequency of ion-pair substructures in proteins is quantitatively related to electrostatic potential: a statistical model for nonbonded interactions

1 reference

https://pubmed.ncbi.nlm.nih.gov/10048326

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Search for the most stable folds of protein chains: I. Application of a self-consistent molecular field theory to a problem of protein three-dimensional structure prediction

1 reference

https://pubmed.ncbi.nlm.nih.gov/10048326

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1110/PS.8.2.326

1 reference

Europe PubMed Central

13 August 2017

1 reference

Europe PubMed Central

13 August 2017

1 reference

Europe PubMed Central

13 August 2017

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