> Tag > Links tagged with 'protein sequence analysis'

Links tagged with 'protein sequence analysis'

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Found 226 links

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MODiTool Content

http://prix.uos.ac.kr/research.jsp [open in a new window]

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Protein > Biochemical Features
Protein > Proteomics

Modi is a tool that facilitates the interpretation of tandem mass spectra in order to identify post-translational modifications (PTMs) in a peptide.

links directory index: 31
TitlePublication YearGoogle Scholar Citation Count
MODi: a powerful and convenient web server for identifying multiple post-translational peptide modifications from tandem mass spectra200631
NAR Web Server Issue 2006
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tagsmass spectrometry peptides post-translational protein processing protein databases protein sequence analysis

MPI ToolkitTool Content

http://toolkit.tuebingen.mpg.de [open in a new window]

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DNA > Phylogeny Reconstruction
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching and Classification

Max-Planck Institute Bioinformatics Toolkit provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction.

This content is being maintained by mremmert.

links directory index: 81
TitlePublication YearGoogle Scholar Citation Count
The MPI Bioinformatics Toolkit for protein sequence analysis200681
NAR Web Server Issue 2006
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tagscomputational biology protein conformation protein sequence analysis proteins sequence alignment

Multi-HarmonyTool Content

http://www.ibi.vu.nl/programs/shmrwww [open in a new window]

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Protein > Sequence Comparison
Protein > Sequence Features
Sequence Comparison > Multiple Sequence Alignments

Multi-Harmony is an interactive web server for detecting sub-type specific sites in proteins starting from a multiple sequence alignment. Combines Sequence Harmony and Multi-Relief methods.

links directory index: 7
TitlePublication YearGoogle Scholar Citation Count
Multi-Harmony: detecting functional specificity from sequence alignment20107
NAR Web Server Issue 2010
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tagsalgorithms protein sequence analysis sequence alignment smad proteins

MutDBDatabase Content

http://www.mutdb.org/ [open in a new window]

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DNA > Annotations
DNA > Sequence Polymorphisms

MutDB is a database that associates protein structural information with mutations and polymorphisms in gene sequences. The data is derived from dbSNP and Swiss-Prot, and can be browsed by gene name or searched by keyword or by various identifiers.

links directory index: 64
TitlePublication YearGoogle Scholar Citation Count
MutDB services: interactive structural analysis of mutation data200533
MutDB: annotating human variation with functionally relevant data200331
NAR Web Server Issue 2005
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tagsamino acid substitution database management systems documentation genetic databases genetic predisposition to disease genetic variation human genome humans molecular models mutation phenotype protein conformation protein databases protein sequence analysis proteins sequence alignment single nucleotide polymorphism structure-activity relationship

MyHitsTool Content

http://myhits.isb-sib.ch [open in a new window]

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Protein > Domains and Motifs
Sequence Comparison > Multiple Sequence Alignments

The MyHits server integrates several tools with a focus on protein annotation and the analysis of protein domains. Guest users have access to tools such as ClustalW and T-Coffee and databases like Swiss-Prot, Prosite and Interpro. Registration allows users to store their results in private databases, and is free for academic users.

This content is being maintained by myhits.

links directory index: 109
TitlePublication YearGoogle Scholar Citation Count
MyHits: improvements to an interactive resource for analyzing protein sequences200738
MyHits: a new interactive resource for protein annotation and domain identification200471
NAR Web Server Issue 2004NAR Web Server Issue 2007
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tagscomputational biology programming languages protein databases protein sequence analysis sequence alignment systems integration tertiary protein structure

NAPSTool Content

http://proteomics.bioengr.uic.edu/NAPS [open in a new window]

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Protein > Sequence Features

NAPS is a web server for the prediction of specific residues involved in nucleic acid-binding proteins (NAPS) binding to nucleic acid. Amino acid residues involved in DNA and RNA binding are predicted.

links directory index: 7
TitlePublication YearGoogle Scholar Citation Count
NAPS: a residue-level nucleic acid-binding prediction server20107
NAR Web Server Issue 2010
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tagsalgorithms binding sites dna-binding proteins protein sequence analysis reproducibility of results rna-binding proteins

NCBI Human DNA Reference SequenceDatabase Content

http://www.ncbi.nlm.nih.gov/RefSeq/ [open in a new window]

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DNA > Sequence Retrieval and Submission
Human Genome > Annotations
Model Organisms > Mouse and Rat
Model Organisms > Yeast

Downloadable human DNA reference sequence as well as other reference genome sequences.

links directory index: 1916
TitlePublication YearGoogle Scholar Citation Count
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy20128
NCBI Reference Sequences: current status, policy and new initiatives2009217
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins2007943
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins2005748
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tagsamino acid sequence animals base sequence dna sequence analysis exons genetic databases genome genomics humans messenger rna mice national library of medicine (u.s.) nucleic acid databases protein databases protein sequence analysis proteins pseudogenes rats reference standards rna sequence analysis sequence analysis systems integration united states untranslated rna

NetCSSPTool Content

http://cssp2.sookmyung.ac.kr [open in a new window]

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Protein > 2-D Structure Prediction

A web application based on contact-dependent secondary structure propensity calculations for predicting chameleon sub-sequences that may contribute to amyloid fibril formation. NetCSSP also contains precalculated non-native secondary structure propensities for 1.4 million fragments of 7 residue length from PDB structures.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
NetCSSP: web application for predicting chameleon sequences and amyloid fibril formation20094
NAR Web Server Issue 2009
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tagsalgorithms amyloid protein sequence analysis secondary protein structure

NeuropredTool Content

http://neuroproteomics.scs.uiuc.edu/neuropred.html [open in a new window]

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Protein > Proteomics
Protein > Sequence Features

NeuroPred is a tool designed to predict cleavage sites at basic amino acid locations in neuropeptide precursor sequences. Neuropred also computes the mass of the predicted peptides with or without selected post-translational modifications.

links directory index: 81
TitlePublication YearGoogle Scholar Citation Count
NeuroPred: a tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptides200654
From precursor to final peptides: a statistical sequence-based approach to predicting prohormone processing200327
NAR Web Server Issue 2006
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tagsamino acid sequence animals aplysia invertebrate hormones logistic models mass spectrometry neuropeptides protein precursors protein sequence analysis regression analysis sensitivity and specificity statistical models

NORSpTool Content

http://cubic.bioc.columbia.edu/services/NORSp/ [open in a new window]

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Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction

NORSp (predictor of NOn-Regular Secondary Structure) is a tool for predicting disordered regions in proteins.

links directory index: 251
TitlePublication YearGoogle Scholar Citation Count
NORSp: Predictions of long regions without regular secondary structure2003106
Loopy proteins appear conserved in evolution2002145
NAR Web Server Issue 2003
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tagsamino acids computational biology conserved sequence genetic transcription hydrogen bonding molecular evolution molecular models pliability protein binding protein databases protein folding protein sequence analysis proteins proteome secondary protein structure software design solvents structure-activity relationship

nsSNPAnalyzerTool Content

http://snpanalyzer.uthsc.edu/ [open in a new window]

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DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

nsSNPAnalyzer is a tool to predict whether a nonsynonymous single nucleotide polymorphism (nsSNP) is phenotypically neutral or disease associated.

links directory index: 43
TitlePublication YearGoogle Scholar Citation Count
nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms200543
NAR Web Server Issue 2005
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tagsalgorithms artificial intelligence computational biology genetic predisposition to disease humans phenotype protein conformation protein sequence analysis sequence alignment single nucleotide polymorphism

oGNMTool Content

http://ignm.ccbb.pitt.edu/GNM_Online_Calculation.htm [open in a new window]

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Protein > Molecular Dynamics and Docking

Online Guassian Network Model (oGNM) calculates the equilibrium dynamics of any structure submitted in PDB format, using the Gaussian Network Model (GNM), a network model for representing biomolecules.

links directory index: 795
TitlePublication YearGoogle Scholar Citation Count
oGNM: online computation of structural dynamics using the Gaussian Network Model200651
iGNM: a database of protein functional motions based on Gaussian Network Model200587
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential1997657
NAR Web Server Issue 2006
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tagsalgorithms binding sites chemical models computational biology computer simulation molecular models molecular structure motion normal distribution nucleic acid conformation oligonucleotides protein binding protein conformation protein databases protein folding protein sequence analysis proteins sequence alignment statistical models structure-activity relationship thermodynamics x-ray crystallography

OpenHUSARTool Content

http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/w2h-open/w2h.open/w2h.start... [open in a new window]

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Protein > 2-D Structure Prediction
Protein > Domains and Motifs
Protein > Localization and Targeting
Sequence Comparison > Similarity Searching and Classification

Open HUSAR (Heidelberg Unix Sequence Analysis Resources) contains suite of bioinformatics pipelines including tasks oriented to protein annotation by homology (ProtSweep), by domain analysis (DomainSweep), and by secondary structure elements (2Dsweep).

links directory index: 7
TitlePublication YearGoogle Scholar Citation Count
ProtSweep, 2Dsweep and DomainSweep: protein analysis suite at DKFZ20077
NAR Web Server Issue 2007
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tagsalgorithms computational biology protein databases protein sequence analysis proteins sequence alignment systems integration tertiary protein structure

PAL2NALTool Content

http://coot.embl.de/pal2nal/ [open in a new window]

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DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Other Alignment Tools

PAL2NAL converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment. Synonymous (Ks) and non-synonymous (Ka) substitution rates can be calculated.

links directory index: 245
TitlePublication YearGoogle Scholar Citation Count
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments2006245
NAR Web Server Issue 2006
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tagscodon dna sequence analysis exons protein sequence analysis sequence alignment

PANTHERDatabase Content

http://www.pantherdb.org [open in a new window]

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Protein > Databases

Protein Analysis THrough Evolutionary Relationships (PANTHER) is a comprehensive software system for inferring the functions of genes based on their evolutionary relationships. Phylogenetic trees of gene families form the basis for PANTHER and these trees are annotated with ontology terms describing the evolution of gene function from ancestral to modern day genes. One of the main applications of PANTHER is in accurate prediction of the functions of uncharacterized genes, based on their evolutionary relationships to genes with functions known from experiment. The PANTHER website also includes software tools for analyzing genomic data relative to known and inferred gene functions.

links directory index: 87
TitlePublication YearGoogle Scholar Citation Count
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium201087
NAR Database Issue 2010
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tagsalgorithms amino acid sequence homology animals computational biology genetic databases humans molecular evolution nucleic acid databases phylogeny protein databases protein sequence analysis tertiary protein structure

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