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Links tagged with 'antibodies'

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ClusProTool Content

http://cluspro.bu.edu/login.php

Protein > Molecular Dynamics and Docking

ClusPro is a tool for automatically computing the docking of two protein structures supplied by the user (or as PDB IDs). The result set is a ranked list of putative complexes, ordered by clustering properties.

NAR Web Server Issue 2004
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tagsalgorithms antibodies antigens binding sites biological models chemical models cluster analysis computational biology discriminant analysis energy transfer enzyme inhibitors fourier analysis molecular dynamics simulation molecular models monte carlo method protein binding protein conformation protein interaction mapping protein multimerization proteins reproducibility of results sensitivity and specificity static electricity time factors

eF-seekTool Content

http://ef-site.hgc.jp/eF-seek/index.jsp

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison

eF-seek predicts protein functional sites by searching for similar electrostatic potential and molecular surface shapes against eF-site, a database of electrostatic surfaces for representative ligand binding sites.

NAR Web Server Issue 2007
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tagsalgorithms antibodies binding sites biological models computational biology computer simulation database management systems ligands molecular models protein conformation protein databases protein folding proteins proteomics s-adenosylhomocysteine static electricity structure-activity relationship three-dimensional imaging trypsin

IEDB-3DDatabase Content

http://www.iedb.org

Protein > Databases

IEDB-3D is the 3D structural component of the Immune Epitope Database (IEDB). IEDB-3D catalogs B- and T-cell epitopes and Major Histocompatibility Complex (MHC) ligands for which 3D structures of complexes with antibodies, T-cell receptors or MHC molecules are available in the Protein Data Bank (PDB). Journal articles that are primary citations of PDB structures and that define immune epitopes are curated within IEDB along with accompanying functional assays and immunologically relevant information. For each curated structure, IEDB-3D provides calculated data on intermolecular contacts and interface areas and includes an application, EpitopeViewer, to visualize the structures. IEDB-3D is fully embedded within IEDB, thus allowing structural data, both curated and calculated, and all accompanying information to be queried using multiple search interfaces. These include queries for epitopes recognized in different pathogens, eliciting different functional immune responses, and recognized by different components of the immune system.

NAR Database Issue 2011
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tagsantibodies antigen receptors b-lymphocyte epitopes epitopes histocompatibility antigens ligands protein conformation protein databases t-lymphocyte epitopes

PatchDockTool Content

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

Protein > Molecular Dynamics and Docking

PatchDock is an algorithm for molecular docking. The input is two molecules of any type: proteins, DNA, peptides, drugs. The output is a list of potential complexes sorted by shape complementarity criteria.

NAR Web Server Issue 2005
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tagsalgorithms alpha-amylases antibodies antigen receptors bacterial proteins binding sites capsid proteins computational biology exotoxins influenza virus hemagglutinin glycoproteins ligands macromolecular substances membrane proteins molecular models multiprotein complexes phosphoenolpyruvate sugar phosphotransferase system protein conformation protein interaction mapping protein-serine-threonine kinases proteins secondary protein structure viral antigens

ZFINDatabase Content

http://zfin.org

Model Organisms > Databases

ZFIN, the Zebrafish Model Organism Database serves as the central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. ZFIN manually curates comprehensive data for zebrafish genes, phenotypes, genotypes, gene expression, antibodies, anatomical structures and publications. A wide-ranging collection of web-based search forms and tools facilitates access to integrated views of these data promoting analysis and scientific discovery. Data formats include text, images and graphical representations.

NAR Database Issue 2011
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tagsanimal models animals antibodies gene expression genetic databases genomics messenger rna phenotype zebrafish