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Links tagged with 'proteins'

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Found 312 links

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3D-JuryTool Content

http://meta.bioinfo.pl/submit_wizard.pl [open in a new window]

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Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs

3D-Jury is a protein structure prediction server that collects predictions from multiple servers and generates the final model using a consensus approach.

links directory index: 775
TitlePublication YearGoogle Scholar Citation Count
ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure2003115
3D-Jury: a simple approach to improve protein structure predictions2003592
Detection of reliable and unexpected protein fold predictions using 3D-Jury200368
NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence homology computer simulation database management systems humans molecular models protein conformation protein databases protein folding protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment tertiary protein structure

3D-partnerTool Content

http://3d-partner.life.nctu.edu.tw/ [open in a new window]

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Protein > 3-D Structural Features
Protein > Networks & Interactions, Pathways and Enzymes

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

links directory index: 27
TitlePublication YearGoogle Scholar Citation Count
3D-partner: a web server to infer interacting partners and binding models200727
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 [open in a new window]

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Protein > 3-D Structure Prediction

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

links directory index: 1748
TitlePublication YearGoogle Scholar Citation Count
Enhanced genome annotation using structural profiles in the program 3D-PSSM20001568
CAFASP-1: critical assessment of fully automated structure prediction methods1999180
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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 [open in a new window]

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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.

links directory index: 98
TitlePublication YearGoogle Scholar Citation Count
3dLOGO: a web server for the identification, analysis and use of conserved protein substructures20073
Query3d: a new method for high-throughput analysis of functional residues in protein structures200536
A structural study for the optimisation of functional motifs encoded in protein sequences20047
Three-dimensional profiles: a new tool to identify protein surface similarities199852
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/ [open in a new window]

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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.

links directory index: 10
TitlePublication YearGoogle Scholar Citation Count
3MATRIX and 3MOTIF: a protein structure visualization system for conserved sequence motifs200310
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/ [open in a new window]

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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.

links directory index: 20
TitlePublication YearGoogle Scholar Citation Count
3MOTIF: visualizing conserved protein sequence motifs in the protein structure database200310
3MATRIX and 3MOTIF: a protein structure visualization system for conserved sequence motifs200310
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 [open in a new window]

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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.

links directory index: 28
TitlePublication YearGoogle Scholar Citation Count
ADGO 2.0: interpreting microarray data and list of genes using composite annotations.20113
ADGO: analysis of differentially expressed gene sets using composite GO annotation200625
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 [open in a new window]

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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.

links directory index: 448
TitlePublication YearGoogle Scholar Citation Count
NetAffx: Affymetrix probesets and annotations2003448
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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 [open in a new window]

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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.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
ALADYN: a web server for aligning proteins by matching their large-scale motion20106
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/ [open in a new window]

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Protein > Domains and Motifs
Sequence Comparison > Similarity Searching and Classification

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

This content is being maintained by raghavagps.

links directory index: 57
TitlePublication YearGoogle Scholar Citation Count
AlgPred: prediction of allergenic proteins and mapping of IgE epitopes200657
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/ [open in a new window]

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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.

links directory index: 26
TitlePublication YearGoogle Scholar Citation Count
AliasServer: a web server to handle multiple aliases used to refer to proteins200426
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tagsalgorithms controlled vocabulary database management systems documentation natural language processing protein databases protein sequence analysis proteins sequence alignment

Align-mTool Content

http://bioinformatics.vub.ac.be/software/software.html [open in a new window]

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Sequence Comparison > Multiple Sequence Alignments

Align-m is an accurate and highly versatile multiple alignment program. It consists of 3 modules, S2P, P2P and P2M (see figure, manual), which can be used separately or consecutively to accomplish several tasks.

links directory index: 81
TitlePublication YearGoogle Scholar Citation Count
Align-m--a new algorithm for multiple alignment of highly divergent sequences200481
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tagsalgorithms amino acid sequence amino acid sequence homology genetic variation molecular sequence data protein sequence analysis proteins reproducibility of results sensitivity and specificity sequence alignment

AlphaPredTool Content

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

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Protein > 2-D Structure Prediction

The AlphaPred server predicts the alpha turn residues in the given protein sequence. The method is based on the neural network training on PSI-BLAST generated position specific matrices and PSIPRED predicted secondary structure.

This content is being maintained by raghavagps.

links directory index: 39
TitlePublication YearGoogle Scholar Citation Count
Prediction of alpha-turns in proteins using PSI-BLAST profiles and secondary structure information200439
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tagsalpha-turns amino acid sequence ANN molecular sequence data neural networks (computer) prediction protein databases protein sequence analysis proteins roc curve secondary protein structure sequence alignment sequence-to-structure network statistical models structure-to-structure network

Andrej Sali LabResource Content

http://salilab.org/our_resources.shtml [open in a new window]

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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).

links directory index: 627
TitlePublication YearGoogle Scholar Citation Count
Tools for comparative protein structure modeling and analysis2003190
Modeller: generation and refinement of homology-based protein structure models2003437
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 [open in a new window]

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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.

links directory index: 29
TitlePublication YearGoogle Scholar Citation Count
ArachnoServer 2.0, an updated online resource for spider toxin sequences and structures201113
ArachnoServer: a database of protein toxins from spiders200916
NAR Database Issue 2011
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tagsanimals protein databases proteins sequence analysis spider venoms spiders

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