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Links tagged with 'multiprotein complexes'

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Found 32 links

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ANCHORTool Content

http://structure.pitt.edu/anchor

Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes

ANCHOR is a web-based tool for the analysis of protein-protein interfaces. ANCHOR indicates possible druggable pockets within the protein using anhor residues.

NAR Web Server Issue 2010
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tagsbinding sites drug discovery multiprotein complexes protein databases protein interaction mapping

BISCDatabase Content

http://bisc.cse.ucsc.edu

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.

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

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.

This content is being maintained by shandar.

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

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.

NAR Database Issue 2011
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tagsmultiprotein complexes protein conformation protein databases proteins

ConPlexTool Content

http://sbi.postech.ac.kr/ConPlex/

Protein > 3-D Structure Comparison

ConPlex is a web server that enables conservation analyses of protein interactions within protein quaternary structures. Results of the residue specific conservation analysis are displayed on the input protein complex structure.

NAR Web Server Issue 2010
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tagsamino acid sequence homology molecular evolution multiprotein complexes quaternary protein structure

CORUMDatabase Content

http://mips.gsf.de/genre/proj/corum

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.

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

Protein > Interactions, Pathways, 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.

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

FiberDockTool Content

http://bioinfo3d.cs.tau.ac.il/FiberDock/

Protein > Molecular Dynamics and Docking

FiberDock is a docking refinement web server that accounts for backbone and side-chain flexibility. Potential docking structures are scored according to an energy function.

NAR Web Server Issue 2010
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tagsalgorithms molecular models multiprotein complexes protein conformation protein interaction mapping

FireDockTool Content

http://bioinfo3d.cs.tau.ac.il/FireDock/

Protein > Molecular Dynamics and Docking

The FireDock web server performs high-throughput flexible refinement and scoring of protein-protein docking solutions. Side chain conformations and rigid body orientations are optimized, and outputs viewed in three-dimensional space.

NAR Web Server Issue 2008
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tagsalgorithms molecular models multiprotein complexes protein interaction mapping

GPU.proton.DOCKTool Content

http://gpudock.orgchm.bas.bg/

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

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.

NAR Web Server Issue 2011
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tagsalgorithms fourier analysis multiprotein complexes mutagenesis protein interaction mapping protons static electricity

GRAMM-XTool Content

http://vakser.bioinformatics.ku.edu/resources/gramm/grammx

Protein > Molecular Dynamics and Docking

GRAMM-X is a protein docking server.

NAR Web Server Issue 2006
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tagsalgorithms antigen-antibody complex automation binding sites computational biology computer simulation dimerization evaluation studies as topic influenza virus hemagglutinin glycoproteins ligands macromolecular substances molecular conformation molecular models multiprotein complexes protein conformation protein databases protein folding protein interaction mapping protein structural homology proteomics reproducibility of results statistical models tertiary protein structure viral antibodies

HexServerTool Content

http://hexserver.loria.fr/

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.

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

Protein > Interactions, Pathways, 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.

NAR Web Server Issue 2010
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tagsbinding sites interleukin-2 interleukin-2 receptors multiprotein complexes protein interaction mapping

I2I-SiteEngineTool Content

http://bioinfo3d.cs.tau.ac.il/I2I-SiteEngine/

Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes

Interface-to-Interface (I2I)-SiteEngine compares pairs of interacting protein binding sites by recognizing similarity of physico-chemical properties and shapes in the protein-protein interfaces.

NAR Web Server Issue 2005
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tagsalgorithms amino acids binding sites computational biology ligands macromolecular substances multiprotein complexes protein conformation protein interaction mapping proteins secondary protein structure

KFC ServerTool Content

http://www.mitchell-lab.org/kfc

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.

NAR Web Server Issue 2008
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tagsartificial intelligence binding sites molecular models multiprotein complexes protein conformation protein interaction mapping