Biochemical functional predictions for protein structures of unknown or uncertain function (Q35214509)

7 August 2017

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title

Biochemical functional predictions for protein structures of unknown or uncertain function (English)

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protein function prediction

7 August 2017

main subject

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protein structure prediction

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Mary Jo Ondrechen

3

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author name string

Caitlyn L Mills

series ordinal

1

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7 August 2017

Penny J Beuning

series ordinal

2

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7 August 2017

publication date

18 February 2015

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Computational and Structural Biotechnology Journal

7 August 2017

published in

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7 August 2017

volume

13

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7 August 2017

page(s)

182-191

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Genetic resources for advanced biofuel production described with the Gene Ontology

7 August 2017

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Standardized description of scientific evidence using the Evidence Ontology (ECO)

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The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes

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13 July 2018

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The Structure-Function Linkage Database

13 July 2018

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Activities at the Universal Protein Resource (UniProt)

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The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases

13 July 2018

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FlyBase 102--advanced approaches to interrogating FlyBase

13 July 2018

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The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations

13 July 2018

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The mouse Gene Expression Database (GXD): 2014 update

13 July 2018

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Ensembl Genomes 2013: scaling up access to genome-wide data

13 July 2018

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The COMBREX project: design, methodology, and initial results

13 July 2018

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The SYSCILIA gold standard (SCGSv1) of known ciliary components and its applications within a systems biology consortium

13 July 2018

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A structural role for the PHP domain in E. coli DNA polymerase III

13 July 2018

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Protein function annotation with Structurally Aligned Local Sites of Activity (SALSAs)

13 July 2018

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Protein function prediction by massive integration of evolutionary analyses and multiple data sources

13 July 2018

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One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012.

13 July 2018

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The Rat Genome Database 2013--data, tools and users

13 July 2018

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A large-scale evaluation of computational protein function prediction

13 July 2018

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PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

13 July 2018

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The use of evolutionary patterns in protein annotation

13 July 2018

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ProBiS-2012: web server and web services for detection of structurally similar binding sites in proteins

13 July 2018

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Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms.

13 July 2018

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Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies

13 July 2018

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Selenomodification of tRNA in archaea requires a bipartite rhodanese enzyme

13 July 2018

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The archaeal COG1901/DUF358 SPOUT-methyltransferase members, together with pseudouridine synthase Pus10, catalyze the formation of 1-methylpseudouridine at position 54 of tRNA.

13 July 2018

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Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing

13 July 2018

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The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

13 July 2018

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GeneDB--an annotation database for pathogens

13 July 2018

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Saccharomyces Genome Database: the genomics resource of budding yeast

13 July 2018

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InterPro in 2011: new developments in the family and domain prediction database

13 July 2018

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An iterative approach of protein function prediction

13 July 2018

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WormBase 2012: more genomes, more data, new website

13 July 2018

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The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata

13 July 2018

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Accelerated Profile HMM Searches

13 July 2018

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PomBase: a comprehensive online resource for fission yeast

13 July 2018

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Characterization of type II and III restriction-modification systems from Bacillus cereus strains ATCC 10987 and ATCC 14579.

13 July 2018

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Diversity of archaeosine synthesis in crenarchaeota

13 July 2018

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The Enzyme Function Initiative

13 July 2018

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Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium

13 July 2018

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Analysis of protein function and its prediction from amino acid sequence

13 July 2018

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HMMER web server: interactive sequence similarity searching

13 July 2018

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Genetic analysis of selenocysteine biosynthesis in the archaeon Methanococcus maripaludis

13 July 2018

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Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity

13 July 2018

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The Mouse Tumor Biology Database (MTB): a central electronic resource for locating and integrating mouse tumor pathology data.

13 July 2018

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Functional classification of protein 3D structures from predicted local interaction sites

13 July 2018

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COMBREX: a project to accelerate the functional annotation of prokaryotic genomes

13 July 2018

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ModBase, a database of annotated comparative protein structure models, and associated resources

13 July 2018

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AgBase: supporting functional modeling in agricultural organisms.

13 July 2018

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ZFIN: enhancements and updates to the Zebrafish Model Organism Database

13 July 2018

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Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes

13 July 2018

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PNPASE regulates RNA import into mitochondria

13 July 2018

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Engineering the enolase magnesium II binding site: implications for its evolution

13 July 2018

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The critical role of RNA processing and degradation in the control of gene expression.

13 July 2018

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Dali server: conservation mapping in 3D

13 July 2018

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Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution

13 July 2018

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Hierarchical classification of gene ontology terms using the GOstruct method

13 July 2018

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Bayesian Markov Random Field analysis for protein function prediction based on network data

13 July 2018

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An overview of in silico protein function prediction.

13 July 2018

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Active site prediction using evolutionary and structural information

13 July 2018

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Annotation error in public databases: misannotation of molecular function in enzyme superfamilies

13 July 2018

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Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure

13 July 2018

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SitesIdentify: a protein functional site prediction tool

13 July 2018

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Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function

13 July 2018

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ResBoost: characterizing and predicting catalytic residues in enzymes

13 July 2018

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INTREPID: a web server for prediction of functionally important residues by evolutionary analysis

13 July 2018

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FINDSITE: a combined evolution/structure-based approach to protein function prediction

13 July 2018

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Protein function annotation by homology-based inference

13 July 2018

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Partial order optimum likelihood (POOL): maximum likelihood prediction of protein active site residues using 3D Structure and sequence properties

13 July 2018

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Annotating proteins with generalized functional linkages

13 July 2018

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The GOA database in 2009--an integrated Gene Ontology Annotation resource

13 July 2018

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13 July 2018

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Structure-based function prediction: approaches and applications.

13 July 2018

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Human polynucleotide phosphorylase reduces oxidative RNA damage and protects HeLa cell against oxidative stress

13 July 2018

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Mechanisms and structures of crotonase superfamily enzymes--how nature controls enolate and oxyanion reactivity

13 July 2018

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ConFunc--functional annotation in the twilight zone

13 July 2018

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Contributions to the NIH-NIGMS Protein Structure Initiative from the PSI Production Centers.

13 July 2018

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KEGG for linking genomes to life and the environment

13 July 2018

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Predicting protein function from sequence and structure

13 July 2018

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Integration of biological networks and gene expression data using Cytoscape

13 July 2018

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Crystal structure of monofunctional histidinol phosphate phosphatase from Thermus thermophilus HB8

13 July 2018

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Prediction and assignment of function for a divergent N-succinyl amino acid racemase

13 July 2018

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Structure-based activity prediction for an enzyme of unknown function

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

siteFiNDER|3D: a web-based tool for predicting the location of functional sites in proteins

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Functional differentiation of proteins: implications for structural genomics.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Selective prediction of interaction sites in protein structures with THEMATICS.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Network-based prediction of protein function

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Computational prediction of cancer-gene function

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

A scalable method for integration and functional analysis of multiple microarray datasets

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Computational solvent mapping reveals the importance of local conformational changes for broad substrate specificity in mammalian cytochromes P450.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Computational approaches for the prediction of protein function in the mitochondrion

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Enhanced automated function prediction using distantly related sequences and contextual association by PFP.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

A gold standard set of mechanistically diverse enzyme superfamilies

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Very fast empirical prediction and rationalization of protein pKa values

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Phydbac "Gene Function Predictor": a gene annotation tool based on genomic context analysis

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Protein molecular function prediction by Bayesian phylogenomics

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

ProFunc: a server for predicting protein function from 3D structure

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Predicting protein function from sequence and structural data.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Pocketome via comprehensive identification and classification of ligand binding envelopes.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Statistical criteria for the identification of protein active sites using Theoretical Microscopic Titration Curves

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Inference of protein function from protein structure.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Automated prediction of protein function and detection of functional sites from structure

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Prediction of protein function using protein-protein interaction data

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Predicting protein function from protein/protein interaction data: a probabilistic approach

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Protein informatics towards function identification

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae).

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Emergence of diverse biochemical activities in evolutionarily conserved structural scaffolds of proteins

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

The Protein Data Bank and structural genomics

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Prediction of Human Protein Function from Post-translational Modifications and Localization Features

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Enzyme function less conserved than anticipated.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

THEMATICS: a simple computational predictor of enzyme function from structure

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Initial sequencing and analysis of the human genome

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

The Sequence of the Human Genome

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Design of high-throughput methods of protein production for structural biology

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Gene ontology: tool for the unification of biology

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Detecting protein function and protein-protein interactions from genome sequences

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

The relationship between protein structure and function: a comprehensive survey with application to the yeast genome

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Histidinol phosphate phosphatase, catalyzing the penultimate step of the histidine biosynthesis pathway, is encoded by ytvP (hisJ) in Bacillus subtilis

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

An evolutionary trace method defines binding surfaces common to protein families

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

A method to predict functional residues in proteins

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

The neighbor-joining method: a new method for reconstructing phylogenetic trees

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

High-resolution (1.5 A) crystal structure of phospholipase C from Bacillus cereus

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Reaction mechanism of alkaline phosphatase based on crystal structures. Two-metal ion catalysis

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

The role of the PHP domain associated with DNA polymerase X from Thermus thermophilus HB8 in base excision repair.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

INTREPID--INformation-theoretic TREe traversal for Protein functional site IDentification

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Using Dali for structural comparison of proteins.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Evaluation of features for catalytic residue prediction in novel folds

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Improved gapped alignment in BLAST.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Prediction of active sites for protein structures from computed chemical properties.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

The importance of porE and porF in the anabolic pyruvate oxidoreductase of Methanococcus maripaludis

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

How Well is Enzyme Function Conserved as a Function of Pairwise Sequence Identity?

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Using a neural network and spatial clustering to predict the location of active sites in enzymes

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Global protein function prediction from protein-protein interaction networks

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Analysis of catalytic residues in enzyme active sites

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

Conservation helps to identify biologically relevant crystal contacts

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4372640

A probabilistic functional network of yeast genes

26 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25848497

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Percolation of annotation errors through hierarchically structured protein sequence databases

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25848497

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.CSBJ.2015.02.003

1 reference

7 August 2017

1 reference

7 August 2017

1 reference