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Links tagged with 'amino acids'

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Found 48 links

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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

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

BindNTool Content

http://bioinformatics.ksu.edu/bindn/

Protein > Domains and Motifs
Protein > Sequence Features

BindN takes an amino acid sequence as input and predicts potential DNA or RNA-binding residues using support vector machines (SVMs).

NAR Web Server Issue 2006
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tagsamino acids artificial intelligence binding sites dna dna-binding proteins molecular models protein sequence analysis rna-binding proteins

CanPredictTool Content

http://www.cgl.ucsf.edu/Research/genentech/canpredict/

Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Protein > Sequence Features

CanPredict uses a combination of computational methods to predict whether specific sequence changes in a protein are likely to be cancer-associated mutations.

NAR Web Server Issue 2007
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tagsalgorithms alleles amino acids computational biology expressed sequence tags genetic predisposition to disease humans missense mutation neoplasm dna neoplasms single nucleotide polymorphism tumor cell line

CASTpTool Content

http://sts.bioengr.uic.edu/castp/

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing

Computed Atlas of Surface Topography of proteins (CASTp) locates and measures concave surface regions on 3D protein structures. This tool can be used to study surface features, binding sites, and functional regions of proteins.

NAR Web Server Issue 2003NAR Web Server Issue 2006
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tagsalgorithms amino acids bacterial proteins bacteriorhodopsins binding sites enzymes ligands macromolecular substances mathematical computing molecular models myoglobin nucleic acid conformation protein conformation protein databases protein sequence analysis proteins ribonucleases sequence alignment single nucleotide polymorphism tertiary protein structure

COILSTool Content

http://www.ch.embnet.org/software/COILS_form.html

Protein > 2-D Structure Prediction

Prediction of coiled coil regions.

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tagsamino acid sequence amino acids animals factual databases humans probability protein conformation proteins

ConSeqTool Content

http://conseq.bioinfo.tau.ac.il/

Protein > 3-D Structural Features
Protein > Phylogeny Reconstruction
Protein > Sequence Features

ConSeq is a tool for predicting functionally and structurally important amino acid residues in protein sequences. The predictions are based on the assumptions that residues of functional importance are often conserved and solvent-accessible, and those of structural importance are often conserved and located in the protein core. A multiple sequence alignment is used to predict the relative solvent accessibility state and the evolutionary rate at each residue. ConSeq has been integrated into ConSurf (2010).

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tagsalgorithms amino acid sequence amino acid sequence homology amino acid substitution amino acids molecular sequence data protein sequence analysis proteins sequence alignment structure-activity relationship

ConSurfTool Content

http://consurf.tau.ac.il/

Protein > 3-D Structural Features
Sequence Comparison > Analysis of Aligned Sequences

The ConSurf server allows one to map levels of amino acid conservation to known protein structures in order to study areas of potential functional importance on the surface of the protein. A PDB file is required as input, and a multiple sequence alignment is optional. If an alignment is not provided, ConSurf will build one by performing a search for homologous sequences and then aligning them. ConSurf 2010 combines ConSurf and ConSeq for an easier, more intuitive interface.

NAR Web Server Issue 2005NAR Web Server Issue 2010
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tagsamino acid sequence amino acid sequence homology amino acid substitution amino acids bacterial proteins base sequence bayes theorem bcl-x protein conserved sequence molecular evolution molecular models nucleic acid conformation phylogeny potassium channels protein conformation protein databases protein sequence analysis proteins proto-oncogene proteins c-bcl-2 sequence alignment sequence analysis

DeNovoIDDatabase Content

http://proteomics.mcw.edu/denovoid/

Protein > Proteomics

DeNovoID is a tool for protein identification using de novo peptide sequence data from mass spectrometry experiments.

NAR Web Server Issue 2005
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tagsalgorithms amino acids mass spectrometry peptides protein databases protein sequence analysis proteomics

DEPTHTool Content

http://mspc.bii.a-star.edu.sg/depth

Protein > Biochemical Features
Protein > Molecular Dynamics and Docking

DEPTH web tool computes depth and solvent-accessible surface area values for the prediction of small molecule ligand binding cavities in proteins.

NAR Web Server Issue 2011
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tagsamino acids binding sites ligands molecular models peptide hydrolases protein conformation proteins west nile virus

DIALTool Content

http://caps.ncbs.res.in/DIAL/home.html

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

DIAL (Domain Identification Algorithm) is a web server for the automatic identification of structural domains given the three-dimensional coordinates of a protein.

NAR Web Server Issue 2005
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tagsalgorithms amino acid motifs amino acid sequence amino acids aspartic acid endopeptidases calmodulin chemical models cluster analysis database management systems documentation factual databases hydroxymethylbilane synthase molecular models molecular sequence data molecular structure papain porins protein conformation protein databases protein folding protein sequence analysis proteins reproducibility of results secondary protein structure sensitivity and specificity sequence alignment tertiary protein structure x-ray crystallography

enoLOGOSTool Content

http://biodev.hgen.pitt.edu/enologos/

Sequence Comparison > Alignment Editing and Visualization

enoLOGOS creates sequence logos based on a variety of input, including sequence alignments, probability and alignment matrices and energy measurements.

NAR Web Server Issue 2005
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tagsamino acids binding sites dna sequence analysis dna-binding proteins sequence alignment zinc fingers

EVAconTool Content

http://www.pdg.cnb.uam.es/eva/con/index.html

Computer Related > Math and Statistics
Protein > 3-D Structural Features

EVAcon automates the continuous evaluation of inter-residue contact prediction servers. Results can be viewed statically or dynamically generated.

NAR Web Server Issue 2005
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tagsamino acids molecular models protein conformation reproducibility of results

FastContactTool Content

http://structure.pitt.edu/servers/fastcontact/

Protein > Molecular Dynamics and Docking

FastContact is a free energy scoring tool for protein-protein complex structures.

NAR Web Server Issue 2007
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tagsalgorithms amino acids binding sites biological models chemical models computational biology computer simulation hydrogen bonding molecular models protein binding protein conformation protein interaction mapping protein sequence analysis proteins solvents static electricity thermodynamics