Protein function annotation by homology-based inference (Q29048177)

Europe PubMed Central

8 April 2021

Protein function annotation by homology-based inference (English)

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main subject

computational biology

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8 April 2021

2

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Anna Tramontano

9

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Janet Thornton

8

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Christine Orengo

7

object named as

Christine Orengo

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Michal Linial

6

object named as

Michal Linial

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Oliver Redfern

3

object named as

Oliver C Redfern

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author name string

Yaniv Loewenstein

1

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James Watson

4

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Dmitrij Frishman

https://scigraph.springernature.com/pub.10.1186/gb-2009-10-2-207

5

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language of work or name

English

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publication date

2 February 2009

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8 April 2021

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8 April 2021

10

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issue

2

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page(s)

207

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exact match

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cites work

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6 April 2017

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6 April 2017

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Inferring protein domain interactions from databases of interacting proteins

6 April 2017

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6 April 2017

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6 April 2017

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6 April 2017

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3did: interacting protein domains of known three-dimensional structure

6 April 2017

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6 April 2017

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The ProDom database of protein domain families: more emphasis on 3D

6 April 2017

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6 April 2017

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Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions

6 April 2017

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The Database of Interacting Proteins: 2004 update

6 April 2017

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The COG database: an updated version includes eukaryotes

6 April 2017

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Domain combinations in archaeal, eubacterial and eukaryotic proteomes

6 April 2017

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Gene ontology: tool for the unification of biology

6 April 2017

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6 April 2017

The Protein Data Bank

1 reference

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Protein structure alignment by incremental combinatorial extension (CE) of the optimal path

6 April 2017

1 reference

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CATH--a hierarchic classification of protein domain structures

6 April 2017

1 reference

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

6 April 2017

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Protein structure comparison by alignment of distance matrices

6 April 2017

1 reference

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6 April 2017

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The relation between the divergence of sequence and structure in proteins

6 April 2017

1 reference

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Protein structure alignment

6 April 2017

1 reference

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Basic local alignment search tool

6 April 2017

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Comparative assessment of large-scale data sets of protein-protein interactions

6 April 2017

1 reference

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The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data

7 April 2017

1 reference

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Flexible structure alignment by chaining aligned fragment pairs allowing twists

7 April 2017

1 reference

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An evolutionary trace method defines binding surfaces common to protein families

7 April 2017

1 reference

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SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions

7 April 2017

1 reference

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7 April 2017

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De-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features

7 April 2017

1 reference

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Prediction of enzyme function based on 3D templates of evolutionarily important amino acids.

3 June 2018

1 reference

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CATHEDRAL: a fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures.

3 June 2018

1 reference

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3 June 2018

1 reference

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DIMA 2.0--predicted and known domain interactions

3 June 2018

1 reference

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Progress from CASP6 to CASP7.

3 June 2018

1 reference

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DOMINE: a database of protein domain 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=2688287

Integrating sequence and structural biology with DAS

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

Assessment of predictions submitted for the CASP7 domain prediction category.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

Structural genomics: keeping up with expanding knowledge of the protein universe

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

Towards fully automated structure-based function prediction in structural genomics: a case study

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

New developments in the InterPro database

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

How complete are current yeast and human protein-interaction networks?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

EVEREST: a collection of evolutionary conserved protein domains

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

The SUPERFAMILY database in 2007: families and functions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein 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=2688287

JAFA: a protein function annotation meta-server

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

Revisiting the prediction of protein function at CASP6.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

Integrating biological data through the genome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

The role of molecular modelling in biomedical research

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

The prediction of protein function at CASP6.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

Effective function annotation through catalytic residue conservation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

Inference of protein function from protein 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=2688287

The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

The MIPS mammalian protein-protein interaction database

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on 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=2688287

PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of 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=2688287

PIRSF: family classification system at the Protein Information Resource

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

Prediction of deleterious functional effects of amino acid mutations using a library of structure-based function descriptors

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

Functional sites in protein families uncovered via an objective and automated graph theoretic approach

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

Recognition of spatial motifs in protein structures

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

Protein clefts in molecular recognition and 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=2688287

Threading a database of protein cores

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

A large-scale experiment to assess protein structure prediction methods.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

Characterizing the microenvironment surrounding protein sites

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

Methods of remote homology detection can be combined to increase coverage by 10% in the midnight zone

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

SURF'S UP! - protein classification by surface comparisons.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

Automated discovery of 3D motifs for protein function annotation

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

The predictive power of the CluSTr database.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

Ten thousand interactions for the molecular biologist

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2688287

A domain interaction map based on phylogenetic profiling

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19226439

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/GB-2009-10-2-207

1 reference

Dimensions Publication ID

3302832

1040399255

0 references

3302832

1 reference

1 reference

1 reference