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Links tagged with 'proteins'

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Found 360 links

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3D-partnerTool Content

http://3d-partner.life.nctu.edu.tw/

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

3D-partner is a tool to predict interacting partners and binding models of a query protein sequence through the analysis of structural complexes.

NAR Web Server Issue 2007
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tagsamino acid sequence amino acid sequence homology binding sites gene expression profiling molecular sequence data protein binding protein databases protein interaction mapping protein sequence analysis proteins saccharomyces cerevisiae saccharomyces cerevisiae proteins tertiary protein structure

3D-pssmTool Content

http://www.sbg.bio.ic.ac.uk/~3dpssm/index2.html

Protein > 3-D Structure Prediction

Protein fold recognition using 1d and 3d sequence profiles coupled with secondary structure and solvation potential information.

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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial genome bacterial proteins computational biology factual databases flavoproteins integrases molecular models molecular sequence data mycoplasma open reading frames protein folding proteins proteome reproducibility of results retroviridae proteins ribonuclease h secondary protein structure sequence alignment solvents structure-activity relationship

3dLOGOTool Content

http://3dlogo.uniroma2.it/3dLOGO/home.html

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Domains and Motifs

3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures.

NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs amino acid sequence animals automation binding sites computational biology computer simulation conserved sequence factual databases false negative reactions humans molecular models molecular structure programming languages protein conformation protein databases protein folding protein sequence analysis protein structural homology proteins sensitivity and specificity sequence alignment src homology domains statistical models surface properties

3MatrixTool Content

http://motif.stanford.edu/distributions/3matrix/

Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs

3Matrix is a tool for visualizing protein sequence motifs and their properties in 3 dimensions. This tool needs to be downloaded and run locally on your own machine.

This content is being maintained by brutlag.

NAR Web Server Issue 2003
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tagsamino acid motifs amino acids animals conserved sequence molecular models protein conformation protein databases proteins sequence alignment

3MotifTool Content

http://motif.stanford.edu/distributions/3motif/

Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs

3Motif is a tool for visualizing protein sequence motifs and their properties in 3 dimensions from PDB structure files.

This content is being maintained by brutlag.

NAR Web Server Issue 2003
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tagsamino acid motifs amino acid sequence amino acids animals conserved sequence database management systems molecular models molecular sequence data protein conformation protein databases protein sequence analysis proteins sequence alignment three-dimensional imaging

ADGOTool Content

http://www.btool.org/ADGO2

Expression > Gene Set Analysis
Expression > cDNA, EST, SAGE

ADGO is a web tool that provides composite interpretations for microarray data comparing two sample groups. It also provides composite interpretations and enrichment analysis for lists of genes from diverse sources of biological information.

NAR Web Server Issue 2011
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tagsalgorithms animals biological models cell differentiation computer simulation documentation gene expression profiling genes humans mice molecular sequence annotation oligonucleotide array sequence analysis protein databases proteins rats t-lymphocytes

Affymetrix NetAffx Analysis CenterDatabase Content

http://www.affymetrix.com/analysis/index.affx

Expression > Transcript Expression Analysis

Allows correlation of GeneChip array results with array design and annotation information; provides access to array content information, including probe sequences and gene annotations; free registration is required.

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tagsanimals consensus sequence gene expression profiling genetic databases markov chains oligonucleotide array sequence analysis protein sequence analysis proteins

ALADYNTool Content

http://aladyn.escience-lab.org

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

The ALADYN web server aligns pairs of protein structures by comparing their internal dynamics and detecting regions that sustain similar large-scale movements. Input is the structure files of two proteins.

NAR Web Server Issue 2010
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tagsamyloid precursor protein secretases cysteine endopeptidases exodeoxyribonucleases hiv protease motion protein conformation protein structural homology proteins

AlgPredTool Content

http://www.imtech.res.in/raghava/algpred/

Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

AlgPred predicts allergenic proteins and maps IgE epitopes on allergenic proteins using several different approaches.

This content is being maintained by raghavagps.

NAR Web Server Issue 2006
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tagsalgorithms allergens amino acid motifs amino acids artificial intelligence epitope mapping epitopes immunoglobulin e proteins

AliasServerDatabase Content

http://cbi.labri.fr/outils/alias/

DNA > Sequence Retrieval and Submission
Protein > Sequence Retrieval

A tool for converting identifiers in which multiple aliases are used to refer to sequences. Also available as a stand-alone tool.

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tagsalgorithms controlled vocabulary database management systems documentation natural language processing protein databases protein sequence analysis proteins sequence alignment

Andrej Sali LabResource Content

http://salilab.org/our_resources.shtml

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Molecular Dynamics and Docking

This page contains various resources for comparative protein structure modelling and analysis from the Sali Lab at University of California at San Francisco (UCSF).

NAR Web Server Issue 2003
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tagsamino acid sequence amino acid sequence homology animals bacterial proteins carrier proteins l-lactate dehydrogenase molecular models molecular sequence data protein databases protein folding protein structural homology proteins reproducibility of results sequence alignment sequence homology systems integration tertiary protein structure trichomonas vaginalis

ArachnoServer 2.0Database Content

http://www.arachnoserver.org

Model Organisms > Databases
Protein > Databases

ArachnoServer is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. Key features of ArachnoServer include a molecular target ontology designed specifically for venom toxins, current and historic taxonomic information and a powerful advanced search interface.

This content is being maintained by glennfking.

NAR Database Issue 2011
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tagsanimals protein databases proteins sequence analysis spider venoms spiders

ArrayExpressDatabase Content

http://www.ebi.ac.uk/arrayexpress/

Expression > Transcript Expression Analysis

Public repository for microarray based gene expression data; contains several curated gene expression datasets.

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tagsalgorithms animals computational biology data collection database management systems europe gene expression profiling genetic databases information dissemination information systems oligonucleotide array sequence analysis proteins software design

ASDDatabase Content

http://mdl.shsmu.edu.cn/ASD/

Protein > Databases

AlloSteric Database (ASD) provides a central resource for the display, search and analysis of structure, function and related annotation for allosteric molecules. Proteins are annotated with a detailed description of allostery, biological process and related diseases, and modulators with binding affinity, physicochemical properties and therapeutic area.

NAR Database Issue 2011
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tagsallosteric regulation allosteric site drug design protein databases proteins

ASPicDBDatabase Content

http://www.caspur.it/ASPicDB/

Human Genome > Databases
Protein > Databases

ASPicDB provides a unique annotation resource of human protein variants generated by alternative splicing. A total of 256,939 protein variants from 17,191 multi-exon genes have been extensively annotated through machine learning tools providing information of the protein type (globular and transmembrane), localization, presence of PFAM domains, signal peptides, GPI-anchor propeptides, transmembrane and coiled-coil segments. Furthermore, full-length variants can be now specifically selected based on the annotation of CAGE-tags and polyA signal and/or polyA sites, marking transcription initiation and termination sites, respectively. The retrieval can be carried out at gene, transcript, exon, protein or splice site level allowing the selection of data sets fulfilling one or more features settled by the user.

This content is being maintained by Graziano Pesole.

NAR Database Issue 2011
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tagsalternative splicing exons genetic databases genetic variation humans messenger rna protein isoforms protein sequence analysis proteins