> Tag > Links tagged with 'tertiary protein structure'

Links tagged with 'tertiary protein structure'

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Found 166 links

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NetPhosTool Content

http://www.cbs.dtu.dk/services/NetPhos/ [open in a new window]

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Protein > Sequence Features

NetPhos is a neural network-based method for predicting potential phosphorylation sites at serine, threonine or tyrosine residues in protein sequences

links directory index: 1539
TitlePublication YearGoogle Scholar Citation Count
Sequence and structure-based prediction of eukaryotic protein phosphorylation sites19991539
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tagsamino acid motifs amino acid sequence animals binding sites consensus sequence eukaryotic cells glycosylation molecular models neural networks (computer) nuclear proteins phosphoproteins phosphorylation phylogeny reproducibility of results sensitivity and specificity serine substrate specificity tertiary protein structure threonine trans-activators tyrosine

NRPS-PKSTool Content

http://www.nii.res.in/nrps-pks.html [open in a new window]

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Protein > Domains and Motifs

NRPS-PKS is an tool comprising four integrated databases for the analysis of large multi-enzymatic multi-domain megasynthases. The user can submit a query sequence to search for domains or view the properties of the products.

links directory index: 111
TitlePublication YearGoogle Scholar Citation Count
NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases2004111
NAR Web Server Issue 2004
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tagsmultienzyme complexes peptide synthases protein databases substrate specificity tertiary protein structure

OMPdbDatabase Content

http://bioinformatics.biol.uoa.gr/OMPdb [open in a new window]

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Protein > Databases

OMPdb is a database of integral beta-barrel outer membrane proteins from Gram-negative bacteria, classified in functional families. OMPdb entries contain cross-references to other databases, references to the literature and annotation for sequence features (TM segments and signal peptides). The user can submit text searches and run BLAST queries against protein sequences or domain searches against the collection of profile HMMs that represent each family's domain organization.

This content is being maintained by pbagos.

links directory index: 8
TitlePublication YearGoogle Scholar Citation Count
OMPdb: a database of {beta}-barrel outer membrane proteins from Gram-negative bacteria20118
NAR Database Issue 2011
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external linksLink on Wikipedia
tagsbacterial outer membrane proteins gram-negative bacteria protein databases tertiary protein structure

OpenHUSARTool Content

http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/w2h-open/w2h.open/w2h.start... [open in a new window]

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Protein > 2-D Structure Prediction
Protein > Domains and Motifs
Protein > Localization and Targeting
Sequence Comparison > Similarity Searching and Classification

Open HUSAR (Heidelberg Unix Sequence Analysis Resources) contains suite of bioinformatics pipelines including tasks oriented to protein annotation by homology (ProtSweep), by domain analysis (DomainSweep), and by secondary structure elements (2Dsweep).

links directory index: 7
TitlePublication YearGoogle Scholar Citation Count
ProtSweep, 2Dsweep and DomainSweep: protein analysis suite at DKFZ20077
NAR Web Server Issue 2007
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tagsalgorithms computational biology protein databases protein sequence analysis proteins sequence alignment systems integration tertiary protein structure

OrthoDBDatabase Content

http://cegg.unige.ch/orthodb [open in a new window]

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Protein > Databases

OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across 44 vertebrates, 25 arthropods, and 46 fungi. OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups, and facilitate comprehensive orthology database querying.

links directory index: 18
TitlePublication YearGoogle Scholar Citation Count
OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011201118
NAR Database Issue 2011
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external linksLink on Wikipedia
tagsamino acid sequence homology animals arthropods drosophila melanogaster fungi genes genetic databases genomics mice molecular evolution molecular sequence annotation phylogeny proteins saccharomyces cerevisiae tertiary protein structure vertebrates

PANTHERDatabase Content

http://www.pantherdb.org [open in a new window]

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Protein > Databases

Protein Analysis THrough Evolutionary Relationships (PANTHER) is a comprehensive software system for inferring the functions of genes based on their evolutionary relationships. Phylogenetic trees of gene families form the basis for PANTHER and these trees are annotated with ontology terms describing the evolution of gene function from ancestral to modern day genes. One of the main applications of PANTHER is in accurate prediction of the functions of uncharacterized genes, based on their evolutionary relationships to genes with functions known from experiment. The PANTHER website also includes software tools for analyzing genomic data relative to known and inferred gene functions.

links directory index: 87
TitlePublication YearGoogle Scholar Citation Count
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium201087
NAR Database Issue 2010
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tagsalgorithms amino acid sequence homology animals computational biology genetic databases humans molecular evolution nucleic acid databases phylogeny protein databases protein sequence analysis tertiary protein structure

PatroclesDatabase Content

http://www.patrocles.org [open in a new window]

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DNA > Databases
Human Genome > Databases

The Patrocles database compiles DNA sequence polymorphisms (DSPs) that are predicted to perturb miRNA-mediated gene regulation.

links directory index: 28
TitlePublication YearGoogle Scholar Citation Count
Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates201028
NAR Database Issue 2010
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tagsanimals computational biology gene expression regulation gene silencing genetic databases humans mice micrornas nucleic acid databases quantitative trait loci single nucleotide polymorphism tertiary protein structure

PCDBDatabase Content

http://www.pcdb.unq.edu.ar [open in a new window]

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Protein > Databases

PCDB is a database of protein conformational diversity. For each protein, the database contains the redundant compilation of all the corresponding crystallographic structures obtained under different conditions. These structures could be considered as different instances of protein dynamism. As a measure of the conformational diversity we use the maximum RMSD obtained comparing the structures deposited for each domain. The redundant structures were extracted following CATH structural classification and cross linked with additional information. In this way it is possible to relate a given amount of conformational diversity with different levels of information, such as protein function, presence of ligands and mutations, structural classification, active site information and organism taxonomy among others.

links directory index: 5
TitlePublication YearGoogle Scholar Citation Count
PCDB: a database of protein conformational diversity20115
NAR Database Issue 2011
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tagscrystallography protein databases tertiary protein structure

Pcons.netTool Content

http://pcons.net/ [open in a new window]

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Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching and Classification

Pcons.net is a protein structure prediction meta server that provides automated tools for protein structure prediction and analysis using a consensus approach.

links directory index: 253
TitlePublication YearGoogle Scholar Citation Count
Pcons.net: protein structure prediction meta server200737
Identification of correct regions in protein models using structural, alignment, and consensus information200693
Pcons5: combining consensus, structural evaluation and fold recognition scores200551
Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller200372
NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence animals automatic data processing automation computational biology computer simulation consensus sequence humans molecular models molecular sequence data neural networks (computer) protein conformation protein databases protein folding protein sequence analysis protein structural homology proteins roc curve secondary protein structure sensitivity and specificity sequence alignment statistical models tertiary protein structure

PDBe (formerly MSD)Database Content

http://www.ebi.ac.uk/pdbe/ [open in a new window]

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Protein > Databases

The Protein Data Bank in Europe (PDBe) is the European resource for the collection, organisation and dissemination of data on biological macromolecular structures. The database infrastructure is based on the remediated PDB archive data and a specially designed database for storing information on interactions between proteins and bound molecules. The newly designed 'PDBeView Atlas pages' provide an overview of an individual PDB entry in a user-friendly layout and serves as a starting point to further explore the information available in the PDBe database. PDBe's active involvement with the X-ray crystallography, Nuclear Magnetic Resonance spectroscopy and cryo-Electron Microscopy communities have resulted in improved tools for structure deposition and analysis.

links directory index: 51
TitlePublication YearGoogle Scholar Citation Count
PDBe: Protein Data Bank in Europe201051
NAR Database Issue 2010
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tagsamino acid sequence amino acid sequence homology animals binding sites computational biology europe genetic databases humans ligands molecular sequence data protein databases tertiary protein structure

PDBselectDatabase Content

http://bioinfo.tg.fh-giessen.de/pdbselect/ [open in a new window]

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Protein > Databases

PDBselect is a list of representative protein chains with low mutual sequence identity selected from the protein data bank (PDB) to enable unbiased statistics. PDBfilter-select is an online service to generate user-defined selections.

links directory index: 22
TitlePublication YearGoogle Scholar Citation Count
PDBselect 1992-2009 and PDBfilter-select201022
NAR Database Issue 2010
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tagsanimals computational biology genetic databases humans online systems protein databases proteins tertiary protein structure

PDBSiteScanTool Content

http://wwwmgs.bionet.nsc.ru/mgs/systems/fastprot/pdbsitescan.html [open in a new window]

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Protein > 3-D Structural Features

PDBSiteScan takes a PDB file as input, and searches for stuctural matches with the PDBSite set of known functional sites.

links directory index: 63
TitlePublication YearGoogle Scholar Citation Count
PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins200463
NAR Web Server Issue 2004
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tagsbinding sites catalytic domain hydrolases intracellular signaling peptides and proteins molecular models oncogene proteins post-translational protein processing proteins tertiary protein structure

PepStrTool Content

http://www.imtech.res.in/raghava/pepstr/ [open in a new window]

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Other Molecules > Peptides
Protein > Sequence Features

The Pepstr server predicts the tertiary structure of small peptides with sequence length varying between 7 to 25 residues. The prediction strategy is based on the realization that β-turn is an important and consistent feature of small peptides in addition to regular structures. Thus, the methods uses both the regular secondary structure information predicted from PSIPRED and β-turns information predicted from BetaTurns.

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links directory index: 17
TitlePublication YearGoogle Scholar Citation Count
PEPstr: a de novo method for tertiary structure prediction of small bioactive peptides200717
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tagsbeta-turns bioactive ligands monte carlo method peptides protein binding tertiary protein structure tertiary structure prediction

PeptidomeDatabase Content

ftp://ftp.ncbi.nih.gov/pub/peptidome/ [open in a new window]

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Protein > Databases
Protein > Proteomics

Peptidome is a public repository that archives and freely distributes tandem mass spectrometry peptide and protein identification data generated by the scientific community. Data from all stages of a mass spectrometry experiment are captured, including original mass spectra files, experimental metadata and conclusion-level results.

links directory index: 17
TitlePublication YearGoogle Scholar Citation Count
NCBI Peptidome: a new repository for mass spectrometry proteomics data201017
NAR Database Issue 2010
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tagscomputational biology gene expression profiling genetic databases humans mass spectrometry national library of medicine (u.s.) nucleic acid databases peptides protein databases proteomics tertiary protein structure united states

PepXDatabase Content

http://pepx.switchlab.org/pepx/ [open in a new window]

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Protein > Databases

PepX is an exhaustive data set of all protein-peptide complexes available in the Protein Data Bank with peptide lengths up to 35 residues. Complexes have been clustered based on their binding interfaces rather than sequence homology, providing a set of structurally diverse protein-peptide interactions. Each complex is annotated with both biological and structural information. Peptides are also annotated with naturally occurring backbone variations using fragment clusters from the BriX database to aid peptide design.

links directory index: 18
TitlePublication YearGoogle Scholar Citation Count
PepX: a structural database of non-redundant protein-peptide complexes201018
NAR Database Issue 2010
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tagsanimals computational biology humans ligands peptides protein databases protein interaction mapping proteins signal transduction tertiary protein structure

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