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Links tagged with 'proteins'

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Found 312 links

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TreeSAAPTool Content

http://dna.cs.byu.edu/treesaap/ [open in a new window]

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Sequence Comparison > Analysis of Aligned Sequences

The software program TreeSAAP measures the selective influences on 31 structural and biochemical amino acid properties during clade-genesis, and performs goodness-of-fit and categorical statistical tests.

links directory index: 78
TitlePublication YearGoogle Scholar Citation Count
TreeSAAP: selection on amino acid properties using phylogenetic trees200378
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tagsamino acid sequence genetic variation molecular evolution molecular sequence data phylogeny protein sequence analysis proteins

TSEMATool Content

http://tsema.bioinfo.cnio.es/ [open in a new window]

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Protein > Networks & Interactions, Pathways and Enzymes
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences

The Server for Efficient Mapping Assessment (TSEMA) predicts possible protein-protein interactions based on the comparision of phylogenetic trees derived from sequences of associated protein families.

links directory index: 325
TitlePublication YearGoogle Scholar Citation Count
TSEMA: interactive prediction of protein pairings between interacting families200616
Similarity of phylogenetic trees as indicator of protein-protein interaction2001309
NAR Web Server Issue 2006
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tagsbacterial genome chaperonin 60 computational biology escherichia coli proteins glutamate-trna ligase gtp-binding proteins molecular evolution monte carlo method phylogeny protein interaction mapping protein sequence analysis proteins proteome ribosomal proteins sequence alignment statistics as topic tertiary protein structure

UniqueProtTool Content

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

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Protein > Sequence Retrieval

UniqueProt creates representative protein sequence sets by eliminating sequence redundancy based on sequence similiarity. This tool needs to be downloaded and run locally on your own machine.

links directory index: 83
TitlePublication YearGoogle Scholar Citation Count
UniqueProt: Creating representative protein sequence sets200383
NAR Web Server Issue 2003
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tagsalgorithms protein sequence analysis proteins sequence alignment tertiary protein structure

Universal Protein Resource (UniProt)Database Content

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

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Protein > Databases

Universal Protein Resource (UniProt) maintains a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces freely accessible to the scientific community. UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database.

links directory index: 1408
TitlePublication YearGoogle Scholar Citation Count
Reorganizing the protein space at the Universal Protein Resource (UniProt)201213
Ongoing and future developments at the Universal Protein Resource2011154
The Universal Protein Resource (UniProt) in 2010201053
The Universal Protein Resource (UniProt)20071170
Update on genome completion and annotations: Protein Information Resource200418
NAR Database Issue 2010NAR Database Issue 2011
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tagsalgorithms amino acid sequence animals computational biology europe fungal genome human genome humans nucleic acid databases protein databases protein isoforms protein sequence analysis proteins proteome proteomics systems integration viral genome

VADARTool Content

http://redpoll.pharmacy.ualberta.ca/vadar/ [open in a new window]

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

Volume, Area, Dihedral Angle Reporter (VADAR) is a web server for qualitative evaluation of protein structure data.

links directory index: 189
TitlePublication YearGoogle Scholar Citation Count
VADAR: a web server for quantitative evaluation of protein structure quality2003189
NAR Web Server Issue 2003
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tagsalgorithms hydrogen bonding molecular structure protein databases protein folding protein sequence analysis proteins reproducibility of results secondary protein structure

VnDDatabase Content

http://vnd.kobic.re.kr:8080/VnD/ [open in a new window]

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Other Molecules > Databases

The variations and drugs (VnD) is a consolidated database containing information on diseases, related genes and genetic variations, protein structures and drug information. The VnD database is a useful platform for researchers studying the underlying mechanism for association among genetic variations, diseases and drugs.

links directory index: 5
TitlePublication YearGoogle Scholar Citation Count
VnD: a structure-centric database of disease-related SNPs and drugs20115
NAR Database Issue 2011
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tagsdisease genetic databases humans mutation pharmaceutical preparations protein conformation proteins single nucleotide polymorphism

WDACTool Content

http://pat.kobic.re.kr/wdac/index.htm [open in a new window]

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Protein > Domains and Motifs
Protein > Sequence Comparison

The WDAC (Weighted Domain Architecture Comparison Tool) is a web-based server to perform protein homology search by comparing protein domain architectures, defined as a sequential order of domains in a protein.

links directory index: 16
TitlePublication YearGoogle Scholar Citation Count
Protein comparison at the domain architecture level20098
DAhunter: a web-based server that identifies homologous proteins by comparing domain architecture20088
NAR Web Server Issue 2008
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tagscomputational biology protein databases protein sequence analysis protein structural homology proteins tertiary protein structure

WebFEATURETool Content

http://feature.stanford.edu/webfeature/ [open in a new window]

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Protein > 3-D Structural Features
Protein > Domains and Motifs
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

WebFEATURE is a structural analysis tool for identifying 3D physiochemical motifs in molecular structures.

links directory index: 121
TitlePublication YearGoogle Scholar Citation Count
WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular structures200364
Recognizing protein binding sites using statistical descriptions of their 3D environments199857
NAR Web Server Issue 2003
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tagsalgorithms bayes theorem binding sites calcium calcium-binding proteins computational biology factual databases genomics likelihood functions macromolecular substances molecular models molecular structure nucleic acid conformation nucleic acids protein conformation proteins reproducibility of results sensitivity and specificity statistical models

webPIPSATool Content

http://pipsa.h-its.org [open in a new window]

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Protein > Annotation and Function
Protein > Molecular Dynamics and Docking

webPIPSA is the web server for Protein Interaction Property Similarity Analysis (PIPSA), a procedure for the comparison and analysis of protein electrostatic potentials for a large number of related protein structures. The resulting matrices of pairwise electrostatic similarities may be visualized as epograms or heat maps.

This content is being maintained by wade.

links directory index: 66
TitlePublication YearGoogle Scholar Citation Count
SYCAMORE--a systems biology computational analysis and modeling research environment200817
webPIPSA: a web server for the comparison of protein interaction properties200831
qPIPSA: relating enzymatic kinetic parameters and interaction fields200718
NAR Web Server Issue 2008
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tagsalgorithms binding sites biological models chemical models computer simulation electrostatics enzyme activation enzymes kinetics protein binding protein conformation protein interaction mapping proteins research signal transduction static electricity systems biology triose-phosphate isomerase

WebScipio - eukaryotic gene identificationTool Content

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

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DNA > Gene Prediction
Expression > Splicing
RNA > General Resources
Sequence Comparison > Analysis of Aligned Sequences

Scipio is a tool to determine the precise exon-intron gene structure given a protein sequence and a genome. It identifies splice sites and is able to cope with sequencing errors and genes spanning several contigs. The output contains information about discrepancies that may result from sequencing errors. Scipio has also successfully been used to find homologous genes in related species. WebScipio, allows to search for mutually exclusive spliced exons and tandemly arrayed gene duplicates.

links directory index: 24
TitlePublication YearGoogle Scholar Citation Count
WebScipio: an online tool for the determination of gene structures using protein sequences20089
Scipio: using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species200815
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tagsacetylcholine action potentials algorithms alternative splicing amino acid sequence animals apomorphine atropine base sequence benserazide bromocriptine central nervous system dextroamphetamine diaphragm dna sequence analysis dopamine drosophila melanogaster drosophila proteins epinephrine exon-intron structure exons extrapyramidal tracts female gene duplicates gene prediction gene structure genetic databases genomics haloperidol human parainfluenza virus 3 humans hydroxylamines immunologic deficiency syndromes infant introns kinetics levodopa mathematics molecular sequence data motor activity muscle contraction muscle denervation mutually exclusive splicing nerve degeneration neurological models neuromuscular junction nucleic acid sequence homology oxidation-reduction paramyxoviridae infections physostigmine piribedil planarians protein sequence analysis proteins rats reading frames reserpine rna splice sites sequence alignment software species specificity superoxide dismutase superoxides synaptic transmission tandem gene duplication tetrodotoxin turbellaria user-computer interface viral pneumonia x chromosome

WoLF PSORTTool Content

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

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Protein > Localization and Targeting

WoLF PSORT is an extension of the PSORT II program for protein subcellular location prediction.

links directory index: 463
TitlePublication YearGoogle Scholar Citation Count
WoLF PSORT: protein localization predictor2007463
NAR Web Server Issue 2007
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tagsarabidopsis computational biology humans membrane proteins programming languages protein databases protein sequence analysis protein sorting signals proteins reproducibility of results secondary protein structure statistical models

YLocTool Content

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

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Protein > Localization and Targeting

YLoc is a web server for the prediction of subcellular localization. Predictions are explained and biological properties used for the prediction highlighted. In addition, a confidence estimates rates the reliability of individual predictions.

This content is being maintained by sebastian_v_b.

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
YLoc--an interpretable web server for predicting subcellular localization201011
NAR Web Server Issue 2010
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tagsanimals fungal proteins organelles plant proteins protein sequence analysis proteins reproducibility of results

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