> Tag > Links tagged with 'multiprotein complexes'

Links tagged with 'multiprotein complexes'

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Found 21 links

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BISCDatabase Content

http://bisc.cse.ucsc.edu [open in a new window]

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Protein > Databases

Binary subcomplexes in proteins database (BISC) is a protein-protein interaction (PPI) database linking up the two communities most active in their characterization: structural biology and functional genomics researchers. The BISC resource offers users (i) a structural perspective and related information about binary subcomplexes (i.e. physical direct interactions between proteins) that are either structurally characterized or modellable entries in the main functional genomics PPI databases BioGRID, IntAct and HPRD; (ii) selected web services to further investigate the validity of postulated PPI by inspection of their hypothetical modelled interfaces.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
BISC: binary subcomplexes in proteins database20111
NAR Database Issue 2011
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tagsgenetic databases genomics molecular models multiprotein complexes protein databases protein interaction mapping

CCRXPTool Content

http://ccrxp.netasa.org [open in a new window]

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Protein > 3-D Structural Features
Protein > Sequence Features

A tool for the detection of conserved residue clusters from an input PDB file. Structural properties of each residue, such as solvent accessibility (ASA), secondary structure, conservation score etc. and the conserved residue clusters are also computed.

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links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
CCRXP: exploring clusters of conserved residues in protein structures20103
NAR Web Server Issue 2010
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tagsclustered residues consensus sequence conservation score dna-binding proteins hot spots interface multiprotein complexes mutation proteins rna-binding proteins solvent accessibility

CDDBDatabase Content

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

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Protein > Databases

The conformational dynamics data bank (CDDB) is a database for comprehensive results on the conformational dynamics of high molecular weight proteins and protein assemblies. Analysis is performed using a coarse-grained computational approach that is applied to the majority of structures present in the electron microscopy data bank (EMDB). Results include equilibrium thermal fluctuations and elastic strain energy distributions that identify rigid versus flexible protein domains generally, as well as those associated with specific functional transitions, and correlations in molecular motions that identify molecular regions that are highly coupled dynamically. The data bank is maintained and updated automatically to include conformational dynamics results for new structural entries as they become available in the EMDB.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
Conformational dynamics data bank: a database for conformational dynamics of proteins and supramolecular protein assemblies20112
NAR Database Issue 2011
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tagsmultiprotein complexes protein conformation protein databases proteins

CORUMDatabase Content

http://mips.gsf.de/genre/proj/corum [open in a new window]

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Protein > Databases

CORUM is a database that provides a manually curated repository of experimentally characterized protein complexes from mammalian organisms, mainly human (64%), mouse (16%) and rat (12%). The CORUM dataset is built from 3198 different genes, representing approximately 16% of the protein coding genes in humans. Each protein complex is described by a protein complex name, subunit composition, function as well as the literature reference that characterizes the respective protein complex. A 'Phylogenetic Conservation' analysis tool allows one to predict the occurrence of protein complexes in different phylogenetic groups.

links directory index: 116
TitlePublication YearGoogle Scholar Citation Count
CORUM: the comprehensive resource of mammalian protein complexes--20092010116
NAR Database Issue 2010
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tagsanimals computational biology genetic databases humans mice multiprotein complexes phylogeny protein databases rats saccharomyces cerevisiae tertiary protein structure

DrugScorePPITool Content

http://cpclab.uni-duesseldorf.de/dsppi [open in a new window]

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Protein > Networks & Interactions, Pathways and Enzymes
Protein > Sequence Features

DrugScorePPI web server performs alanine scanning within a given protein-protein complex in silico. Useful for guiding biological experiments and in the development of protein-protein interaction modulators.

links directory index: 13
TitlePublication YearGoogle Scholar Citation Count
DrugScorePPI webserver: fast and accurate in silico alanine scanning for scoring protein-protein interactions201013
NAR Web Server Issue 2010
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tagsalanine multiprotein complexes mutation protein interaction mapping ral gtp-binding proteins ral guanine nucleotide exchange factor

eNetTool Content

http://ecoli.med.utoronto.ca/ [open in a new window]

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Model Organisms > Microbes

Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. This resource provides a "systems-wide" functional blueprint of a model microbe, with insights into the biological and evolutionary significance of previously uncharacterized proteins.

links directory index: 84
TitlePublication YearGoogle Scholar Citation Count
Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins200984
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tagsbacterial genome escherichia coli escherichia coli proteins multiprotein complexes protein interaction mapping proteome
setsUniversity of Toronto

GPU.proton.DOCKTool Content

http://gpudock.orgchm.bas.bg/ [open in a new window]

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Protein > Molecular Dynamics and Docking
Protein > Networks & Interactions, Pathways and Enzymes

Genuine Protein Ultrafast proton equilibria consistent DOCKing (GPU.proton.DOCK) is a tool for in silico prediction of protein-protein interactions via ultrafast docking that considers electrostatic interactions and proton equilibria effects on the docking partners.

This content is being maintained by alexkant.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
GPU.proton.DOCK: Genuine Protein Ultrafast proton equilibria consistent DOCKing.20111
NAR Web Server Issue 2011
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tagsalgorithms fourier analysis multiprotein complexes mutagenesis protein interaction mapping protons static electricity

HexServerTool Content

http://hexserver.loria.fr/ [open in a new window]

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Protein > Molecular Dynamics and Docking

A FFT-based protein docking server powered by graphics processors, HexServer rapidly produces a ranked list of docking predictions for input PDB protein structures.

links directory index: 28
TitlePublication YearGoogle Scholar Citation Count
HexServer: an FFT-based protein docking server powered by graphics processors201028
NAR Web Server Issue 2010
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tagsalgorithms binding sites multiprotein complexes protein conformation

HotPointTool Content

http://prism.ccbb.ku.edu.tr/hotpoint [open in a new window]

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Protein > Networks & Interactions, Pathways and Enzymes

HotPoint web server predicts hot spots in protein interfaces using an empirical model. Input is a protein complex and two chain identifiers that form an interface; output includes an interactive 3D visualization of the hot spots.

links directory index: 25
TitlePublication YearGoogle Scholar Citation Count
HotPoint: hot spot prediction server for protein interfaces201025
NAR Web Server Issue 2010
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tagsbinding sites interleukin-2 interleukin-2 receptors multiprotein complexes protein interaction mapping

KFC ServerTool Content

http://www.mitchell-lab.org/kfc [open in a new window]

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Protein > 3-D Structural Features

The KFC Server is a web-based implementation of the Knowledge-based FADE and Contacts (KFC) model. KFC predicts the subset of residues responsible for the majority of a protein interface's binding free energy. Users input protein-protein or protein-DNA information for visualization of binding hot spots within the protein structure.

links directory index: 29
TitlePublication YearGoogle Scholar Citation Count
KFC Server: interactive forecasting of protein interaction hot spots200829
NAR Web Server Issue 2008
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tagsartificial intelligence binding sites molecular models multiprotein complexes protein conformation protein interaction mapping

MAGIIC-PROTool Content

http://biominer.bime.ntu.edu.tw/magiicpro/ [open in a new window]

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Protein > Domains and Motifs
Protein > Sequence Features
Sequence Comparison > Multiple Sequence Alignments

MAGIIC-PRO is a tool for detecting patterns in protein sequences. MAGIIC-PRO takes a protein sequence as input and helps users prepare training data for the pattern mining experiments by using Swiss-Prot annotations or by PSI-BLAST. Multiple resources for analysis of the detected patterns are also presented.

links directory index: 16
TitlePublication YearGoogle Scholar Citation Count
MAGIIC-PRO: detecting functional signatures by efficient discovery of long patterns in protein sequences200616
NAR Web Server Issue 2006
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tagsbinding sites ligands molecular models multiprotein complexes protein conformation protein sequence analysis

Multi-QTool Content

http://ms.iis.sinica.edu.tw/Multi-Q-Web/ [open in a new window]

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Protein > Proteomics

Multi-Q provides an automated data analysis tool for multiplexed protein quantitation based on iTRAQ labeling.

links directory index: 66
TitlePublication YearGoogle Scholar Citation Count
The Multi-Q web server for multiplexed protein quantitation200712
Multi-Q: a fully automated tool for multiplexed protein quantitation200654
NAR Web Server Issue 2007
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tagsautomatic data processing computational biology humans ions jurkat cells liquid chromatography mass spectrometry multiprotein complexes peptides protein folding proteins proteomics

MultifitTool Content

http://modbase.compbio.ucsf.edu/multifit/ [open in a new window]

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Protein > 3-D Structure Prediction

MultiFit is a web server for fitting multiple protein structures into their electron microscopy density map. The server takes as input a set of protein structures in the PDB format and an EM density map in the MRC format. The output is an ensemble of models ranked by their quality-of-fit to the density map.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map20111
NAR Web Server Issue 2011
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tagselectron microscopy molecular models multiprotein complexes

PCRPi-DBDatabase Content

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

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Protein > Databases

Presaging Critical Residues in Protein Interfaces Database (PCRPi-DB) is a public repository that archives computationally annotated hot spots in protein complexes for which the 3D structure is known. Hot spots have been annotated using a new and highly accurate computational method developed in the lab. Besides browsing and querying the contents of the database, extensive documentation and links to relevant on-line resources and contents are available to users.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
PCRPi-DB: a database of computationally annotated hot spots in protein interfaces20112
NAR Database Issue 2011
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external linksLink on Wikipedia
tagsalgorithms bacterial proteins beta-lactamases computational biology molecular sequence annotation multiprotein complexes protein conformation protein databases protein interaction mapping

PreBITool Content

http://pre-s.protein.osaka-u.ac.jp/prebi/ [open in a new window]

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Protein > 3-D Structural Features

Prediction of Biological Interfaces (PreBI) is a server for predicting protein-protein interfaces in protein structures that maximizes both the degree of complementarity and the interface area.

links directory index: 77
TitlePublication YearGoogle Scholar Citation Count
PreBI: prediction of biological interfaces of proteins in crystals20065
eF-site and PDBjViewer: database and viewer for protein functional sites200472
NAR Web Server Issue 2006
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tagsdatabase management systems humans hydrophobic and hydrophilic interactions molecular models multiprotein complexes protein conformation protein databases proteins static electricity three-dimensional imaging x-ray crystallography

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