Defining and searching for structural motifs using DeepView/Swiss-PdbViewer (Q30419546)

12 August 2017

Defining and searching for structural motifs using DeepView/Swiss-PdbViewer (English)

1 reference

12 August 2017

Maria U Johansson

1

1 reference

12 August 2017

Vincent Zoete

series ordinal

2

1 reference

12 August 2017

Olivier Michielin

series ordinal

3

1 reference

12 August 2017

Nicolas Guex

series ordinal

4

1 reference

12 August 2017

23 July 2012

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12 August 2017

1 reference

12 August 2017

13

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12 August 2017

173

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2105-13-173

12 August 2017

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Robust recognition of zinc binding sites in proteins.

20 June 2018

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

20 June 2018

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A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing.

20 June 2018

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Crystal structure of apo-calmodulin bound to the first two IQ motifs of myosin V reveals essential recognition features

20 June 2018

1 reference

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Crystal structure of the yeast His6 enzyme suggests a reaction mechanism

20 June 2018

1 reference

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Physically realistic homology models built with ROSETTA can be more accurate than their templates

20 June 2018

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PISCES: recent improvements to a PDB sequence culling server

20 June 2018

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The FoldX web server: an online force field

20 June 2018

1 reference

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Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families

20 June 2018

1 reference

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Inference of protein function from protein structure.

20 June 2018

1 reference

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Blood glucose concentration in caviomorph rodents.

20 June 2018

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Stereochemistry of polypeptide chain configurations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436773

An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436773

PISCES: a protein sequence culling server

20 June 2018

1 reference

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WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular structures

20 June 2018

1 reference

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A model for statistical significance of local similarities in structure.

20 June 2018

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Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436773

Creating structure features by data mining the PDB to use as molecular-replacement models

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436773

A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436773

20 June 2018

The Protein Data Bank

1 reference

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Processing and analysis of CASP3 protein structure predictions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436773

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436773

Protein secondary structure prediction based on position-specific scoring matrices

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436773

Recognition of spatial motifs in protein structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436773

HOMSTRAD: a database of protein structure alignments for homologous families

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436773

Structure calculation of biological macromolecules from NMR data.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436773

Recognizing protein binding sites using statistical descriptions of their 3D environments

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436773

A geometric algorithm to find small but highly similar 3D substructures in proteins.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436773

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436773

Recognition of analogous and homologous protein folds--assessment of prediction success and associated alignment accuracy using empirical substitution matrices.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436773

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436773

Touring protein fold space with Dali/FSSP

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436773

CATH--a hierarchic classification of protein domain structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436773

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436773

Protein structure comparison by alignment of distance matrices

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436773

PHD--an automatic mail server for protein secondary structure prediction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436773

Searching protein structure databases has come of age.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436773

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436773

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436773

Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436773

A new approach to protein fold recognition

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436773

The DxDxDG motif for calcium binding: multiple structural contexts and implications for evolution

20 June 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-173

Protein function prediction using local 3D templates

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-173

Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-173

Efficient identification of side-chain patterns using a multidimensional index tree

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-173

Structure-based de novo prediction of zinc-binding sites in proteins of unknown function

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-173

Least-squares fitting of two 3-d point sets.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3436773

Stable configurations of polypeptide chains

26 November 2018

1 reference

12 December 2020

On the problem of comparing protein structures. Development and applications of a new method for the assessment of structural similarities of polypeptide conformations

1 reference

12 December 2020

Importance of individual side chains for the stability of a protein fold: computational alanine scanning of the insulin monomer

1 reference

12 December 2020

Conserved features in the active site of nonhomologous serine proteases

1 reference

12 December 2020

Alanine scanning mutagenesis of insulin

1 reference

12 December 2020

Identifiers

DOI

10.1186/1471-2105-13-173

1 reference

journals/bmcbi/JohanssonZMG12

12 August 2017

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

12 August 2017

1 reference