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Links tagged with 'viral proteins'

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AD-ENMTool Content

http://enm.lobos.nih.gov

Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Molecular Dynamics and Docking

Analysis of Dynamics of Elastic Network Model (AD-ENM) predicts the conformational changes a given protein structure can undergo.

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tagsactins adenosine triphosphate animals binding sites biophysical phenomena biophysics dictyostelium dna polymerase beta dna-directed rna polymerases elasticity humans kinesin ligands mice molecular conformation molecular models molecular motor proteins myosins nucleotides principal component analysis protein binding protein conformation proton-translocating atpases protozoan proteins secondary protein structure statistical models structure-activity relationship taq polymerase tertiary protein structure theoretical models thermodynamics viral proteins x-ray crystallography

FluGenomeTool Content

http://www.flugenome.org/

Human Genome > Health and Disease
Model Organisms > Other Organisms
Sequence Comparison > Similarity Searching

FluGenome is a tool for determining lineages and genotypes of influenza A viruses.

NAR Web Server Issue 2007
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tagscomputational biology genetic databases genetic polymorphism genomics genotype influenza a virus orthomyxoviridae phylogeny viral genes viral genome viral proteins

GWIDDDatabase Content

http://gwidd.bioinformatics.ku.edu

Protein > Databases

Genome-wide docking database (GWIDD) is an integrated resource for structural studies of protein-protein interactions on the genome scale, which combines the available experimental data with models obtained by docking techniques. Current database version (August 2009) contains 25 559 experimental and modeled 3D structures for 771 organisms spanned over the entire universe of life from viruses to humans. Data are organized in a relational database with user-friendly search interface allowing exploration of the database content by a number of parameters. Search results can be interactively previewed and downloaded as PDB-formatted files, along with the information relevant to the specified interactions.

NAR Database Issue 2010
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tagsanimals computational biology genetic databases genome humans nucleic acid databases protein databases protein interaction mapping tertiary protein structure viral genome viral proteins

PFPTool Content

http://pfp.technion.ac.il/

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

PFP (Patch Finder Plus) is a tool for extracting and displaying positive electrostatic patches on protein surfaces which can be indicative of nucleic acid binding interfaces.

This content is being maintained by shulash3.

NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs amino acid sequence binding sites computational biology dna-binding proteins hydrogen bonding hydrogen-ion concentration molecular conformation molecular models molecular sequence data neural networks (computer) plant proteins programming languages protein binding protein conformation protein databases proteins static electricity surface properties viral proteins

PhEVERDatabase Content

http://pbil.univ-lyon1.fr/databases/phever

Model Organisms > Databases

The PhEVER database provides accurate evolutionary and phylogenetic information to analyse the nature of virus-virus and virus-host lateral gene transfers. It is a database of homologous families both (i) between sequences from different viruses and (ii) between viral sequences and sequences from cellular organisms. It offers a clustering of proteins into homologous families containing at least one viral sequences, as well as alignments and phylogenies for each of these families.

This content is being maintained by Leonor Palmeira.

NAR Database Issue 2011
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tagscluster analysis genetic databases genomics horizontal gene transfer host-pathogen interactions molecular evolution phylogeny sequence homology viral genes viral genome viral proteins viruses

PVSTool Content

http://imed.med.ucm.es/PVS/

Protein > 3-D Structure Retrieval/Viewing

Protein Sequence Variability (PVS) is a web server for the prediction of conserved T-cell epitopes. Several variability metrics are used to compute the absolute site variability in multiple protein sequence alignments.

NAR Web Server Issue 2008
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tagsaids vaccines b-lymphocyte epitopes protein conformation protein sequence analysis proteins sequence alignment t-lymphocyte epitopes viral proteins

ReadOutTool Content

http://gibk26.bio.kyutech.ac.jp/jouhou/readout/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > 3-D Structural Features

Readout is a server for the calculation of direct and indirect readout energy Z-scores which estimate the degree of sequence specificity of the protein-DNA complex. Readout can be useful for checking the quality of protein-DNA interactions in three dimensional (3D) structures.

NAR Web Server Issue 2006
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tagsbacterial proteins base sequence binding sites biological models dimerization dna dna primers dna-binding proteins endonucleases gene expression regulation genetic promoter regions glucocorticoid receptors hydrogen bonding macromolecular substances metalloproteins molecular models nucleic acid conformation protein binding protein conformation protein kinases protein subunits proteins repressor proteins saccharomyces cerevisiae proteins tertiary protein structure thermodynamics type ii site-specific deoxyribonucleases viral proteins viral regulatory and accessory proteins water zinc fingers

The Mendel SiteTool Content

http://mendel.imp.ac.at/

Protein > Biochemical Features
Protein > Domains and Motifs
Protein > Localization and Targeting

The Mendel Site contains a collection of tools for predicting lipid postranslational modifications and localization signals in protein sequences.

NAR Web Server Issue 2003
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tagsacyltransferases amino acid motifs animals eukaryotic cells fungal proteins glycine glycosylphosphatidylinositols lipid metabolism molecular sequence data myristic acids peroxisomes plant proteins post-translational protein processing protein sequence analysis protein sorting signals proteins protozoan proteins viral proteins

TRODTool Content

http://www.cellbio.unige.ch/RNAi.html

DNA > Tools For the Bench
Expression > Gene Regulation
RNA > Structure Prediction, Visualization, and Design

T7 RNAi Oligo Designer (TROD) aids in the design of DNA oligonucleotides for short interfering RNA (siRNA) synthesis with T7 RNA polymerase. It takes an input of a cDNA sequence and outputs a list of DNA oligos for ordering.

NAR Web Server Issue 2004
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tagscell line dna-directed rna polymerases double-stranded rna gene silencing green fluorescent proteins hela cells humans luminescent proteins messenger rna molecular cloning molecular sequence data oligodeoxyribonucleotides plasmids recombinant fusion proteins rna interference small interfering rna transfection viral proteins

Viral BioinformaticsTool Content

http://athena.bioc.uvic.ca/

Model Organisms > Other Organisms
Protein > Sequence Features
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Viral Bioinformatics provides access to viral genomes and a variety of tools for comparative genomic analyses.

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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial genome base composition base sequence biological models canada capripoxvirus chlamydophila pneumoniae cluster analysis computational biology computer systems database management systems dna dna sequence analysis documentation factual databases fuzzy logic genetic databases genome genomics humans molecular evolution molecular sequence data multigene family multimedia mutation nucleic acid databases nucleic acid regulatory sequences nucleotides open reading frames phylogeny poxviridae programming languages protein databases protein sequence analysis reference standards sequence alignment statistical data interpretation systems integration technology transfer thermoplasma vaccinia virus variola virus viral dna viral genes viral genome viral proteins

ViralZoneDatabase Content

http://www.expasy.org/viralzone/

Model Organisms > Databases

ViralZone web resource provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. ViralZone offers a complete set of detailed and accurate virion pictures.

NAR Database Issue 2011
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tagsgenetic databases genomics proteomics viral genome viral proteins virion virus physiological phenomena virus replication viruses

VirHostnetDatabase Content

http://pbildb1.univ-lyon1.fr/virhostnet/login.php

Model Organisms > Microbes
Protein > Interactions, Pathways, Enzymes

Virus-Host Network is a knowledge-base system dedicated to the curation, the integration, the management and the analysis of virus-host molecular (mainly protein-protein) interaction networks as well as their functional annotation (molecular functions, cellular pathways, protein domains). VirHostNet contains high quality and up-to-date information gathered and curated from public databases.

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tagshost-pathogen interactions protein databases protein interaction mapping proteome viral proteins virus diseases virus physiological phenomena