(Q30373443)

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Local descriptors of protein structure: a systematic analysis of the sequence-structure relationship in proteins using short- and long-range interactions

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scholarly article

1 reference

Europe PubMed Central

26 September 2017

Local descriptors of protein structure: a systematic analysis of the sequence-structure relationship in proteins using short- and long-range interactions (English)

1 reference

Europe PubMed Central

26 September 2017

Andriy Kryshtafovych

2

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Torgeir R Hvidsten

1

object named as

Torgeir R Hvidsten

1 reference

Europe PubMed Central

26 September 2017

Krzysztof Fidelis

3

object named as

Krzysztof Fidelis

1 reference

Europe PubMed Central

26 September 2017

language of work or name

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publication date

1 June 2009

1 reference

Europe PubMed Central

26 September 2017

1 reference

Europe PubMed Central

26 September 2017

75

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Europe PubMed Central

26 September 2017

4

1 reference

Europe PubMed Central

26 September 2017

870-884

1 reference

Europe PubMed Central

26 September 2017

Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Progress from CASP6 to CASP7.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Template-based modeling and free modeling by I-TASSER in CASP7.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Analysis of TASSER-based CASP7 protein structure prediction results.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Library of local descriptors models the core of proteins accurately

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Generalized modeling of enzyme-ligand interactions using proteochemometrics and local protein substructures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

The impact of structural genomics: expectations and outcomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Protein-structure prediction by recombination of fragments.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Progress over the first decade of CASP experiments.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Free modeling with Rosetta in CASP6

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Assessment of fold recognition predictions in CASP6.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

CASP6 data processing and automatic evaluation at the protein structure prediction center.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Connecting the protein structure universe by using sparse recurring fragments.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Protein folding and the organization of the protein topology universe.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

A novel approach to fold recognition using sequence-derived properties from sets of structurally similar local fragments of proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Hierarchical protein folding pathways: a computational study of protein fragments.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Protein decoy assembly using short fragments under geometric constraints.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Overview of structural genomics: from structure to function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Extension of a local backbone description using a structural alphabet: a new approach to the sequence-structure relationship.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Small libraries of protein fragments model native protein structures accurately.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

A sphere-based descriptor for matching protein structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

A divide and conquer approach to fast loop modeling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Rosetta in CASP4: progress in ab initio protein structure prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Automated multiple structure alignment and detection of a common substructural motif

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Recurrent oligomers in proteins: an optimal scheme reconciling accurate and concise backbone representations in automated folding and design studies.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

An alternative view of protein fold space

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

The ASTRAL compendium for protein structure and sequence analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Ab initio protein structure prediction of CASP III targets using ROSETTA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Structure-based functional motif identifies a potential disulfide oxidoreductase active site in the serine/threonine protein phosphatase-1 subfamily

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Protein secondary structure prediction based on position-specific scoring matrices

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Twilight zone of protein sequence alignments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Recognition of spatial motifs in protein structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Prediction of local structure in proteins using a library of sequence-structure motifs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: a database for modeling and prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Ab initio structure prediction for small polypeptides and protein fragments using genetic algorithms.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Global properties of the mapping between local amino acid sequence and local structure in proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

A local alignment method for protein structure motifs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Biological meaning, statistical significance, and classification of local spatial similarities in nonhomologous proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Three-dimensional, sequence order-independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: potential implications to evolution and to protein folding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Comparison of systematic search and database methods for constructing segments of protein structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

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=5479691

20 June 2018

Recurring local sequence motifs in proteins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

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=5479691

20 June 2018

Comparison of super-secondary structures in proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Using known substructures in protein model building and crystallography

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Segmentation of a protein into structural elements: analysis and classification of segments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Modelling the polypeptide backbone with 'spare parts' from known protein structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

A 3D building blocks approach to analyzing and predicting structure of proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Automatic definition of recurrent local structure motifs in proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Common spatial arrangements of backbone fragments in homologous and non-homologous proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

Structural patterns in globular proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

β-Sheet topology and the relatedness of proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

20 June 2018

A solution for the best rotation to relate two sets of vectors

1 reference

https://api.crossref.org/works/10.1002%2FPROT.22296

21 January 2018

Structural drift: a possible path to protein fold change

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

26 November 2018

Of men and machines

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

26 November 2018

Quantifying the similarities within fold space

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

26 November 2018

A 'periodic table' for protein structures.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

26 November 2018

Predicting novel protein folds by using FRAGFOLD.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

26 November 2018

Improved protein loop prediction from sequence alone.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

26 November 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

26 November 2018

Linkers of secondary structures in proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

26 November 2018

An automated classification of the structure of protein loops.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5479691

26 November 2018

Protein local structure prediction from sequence

1 reference

https://pubmed.ncbi.nlm.nih.gov/19025980

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Protein fragment clustering and canonical local shapes

1 reference

https://pubmed.ncbi.nlm.nih.gov/19025980

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Canonical structures for the hypervariable regions of immunoglobulins

1 reference

https://pubmed.ncbi.nlm.nih.gov/19025980

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1002/PROT.22296

1 reference

Europe PubMed Central

26 September 2017

1 reference

Europe PubMed Central

26 September 2017

1 reference

Europe PubMed Central

26 September 2017

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