A supersecondary structure library and search algorithm for modeling loops in protein structures (Q33240022)

24 July 2017

title

A supersecondary structure library and search algorithm for modeling loops in protein structures (English)

1 reference

24 July 2017

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Narcis Fernandez-Fuentes

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author name string

Baldomero Oliva

series ordinal

2

1 reference

24 July 2017

András Fiser

series ordinal

3

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24 July 2017

language of work or name

English

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publication date

14 April 2006

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24 July 2017

published in

Nucleic Acids Research

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24 July 2017

volume

34

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24 July 2017

issue

7

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24 July 2017

page(s)

2085-2097

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Protein structure modeling in the proteomics era.

24 July 2017

cites work

1 reference

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28 July 2018

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Pairwise sequence alignment below the twilight zone

28 July 2018

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Automated classification of antibody complementarity determining region 3 of the heavy chain (H3) loops into canonical forms and its application to protein structure prediction.

28 July 2018

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Analysis, clustering and prediction of the conformation of short and medium size loops connecting regular secondary structures

28 July 2018

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Does conformational free energy distinguish loop conformations in proteins?

28 July 2018

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Creation and characterization of a new, non-redundant fragment data bank

28 July 2018

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

28 July 2018

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A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence

28 July 2018

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

28 July 2018

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Structural families in loops of homologous proteins: automatic classification, modelling and application to antibodies

28 July 2018

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Automatic classification and analysis of alpha alpha-turn motifs in proteins

28 July 2018

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Fragment ranking in modelling of protein structure. Conformationally constrained environmental amino acid substitution tables.

28 July 2018

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Comparative protein modelling by satisfaction of spatial restraints

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1440879

Evaluation of the conformational free energies of loops in proteins.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1440879

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

28 July 2018

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28 July 2018

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Calcium-binding proteins 1: EF-hands.

28 July 2018

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Prediction of the occurrence of the ADP-binding beta alpha beta-fold in proteins, using an amino acid sequence fingerprint

28 July 2018

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Using known substructures in protein model building and crystallography

28 July 2018

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

28 July 2018

1 reference

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Modeling antibody hypervariable loops: a combined algorithm.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1440879

Conserved folding in retroviral proteases: crystal structure of a synthetic HIV-1 protease

28 July 2018

1 reference

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The P-loop--a common motif in ATP- and GTP-binding proteins

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1440879

Secondary structure-based profiles: use of structure-conserving scoring tables in searching protein sequence databases for structural similarities

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1440879

Amino acid substitution matrices from protein blocks

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1440879

Prediction of the conformation and geometry of loops in globular proteins: testing ArchDB, a structural classification of loops.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1440879

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1440879

Efficient methods for filtering and ranking fragments for the prediction of structurally variable regions in proteins

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1440879

Recent improvements to the PROSITE database

31 October 2018

1 reference

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Assessment of progress over the CASP experiments

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1440879

DSSPcont: Continuous secondary structure assignments for proteins.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1440879

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1440879

A divide and conquer approach to fast loop modeling

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1440879

Protein structure prediction and structural genomics

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1440879

Improved protein loop prediction from sequence alone

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1440879

FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1440879

Modeling of loops in protein structures

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1440879

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1440879

Structure-based evaluation of sequence comparison and fold recognition alignment accuracy

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1440879

Enhanced conformational diversity search of CDR-H3 in antibodies: role of the first CDR-H3 residue

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1440879

Importance of anchor group positioning in protein loop prediction

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1440879

The packing density in proteins: standard radii and volumes.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1440879

The Eleventh Datta Lecture. The structural basis for substrate recognition and control by protein kinases

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1440879

Interchanges of spatially neighbouring residues in structurally conserved environments

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1440879

An automated classification of the structure of protein loops.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1440879

Protein structure comparison by alignment of distance matrices

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1440879

Comparison of three algorithms for the assignment of secondary structure in proteins: the advantages of a consensus assignment.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1440879

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1440879

Comparative model-building of the mammalian serine proteases

31 October 2018

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12 December 2020

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

1 reference

12 December 2020

Canonical structures for the hypervariable regions of immunoglobulins

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12 December 2020

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

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12 December 2020

Generation of accurate protein loop conformations through low-barrier molecular dynamics

1 reference

12 December 2020

Beta-hairpins in proteins revisited: lessons for de novo design

1 reference

12 December 2020

Predicting antibody hypervariable loop conformations. II: Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations

1 reference

12 December 2020

Sequence alignment approach to pick up conformationally similar protein fragments

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKL156

1 reference

24 July 2017

1 reference

24 July 2017

1 reference