> Tag > Links tagged with 'viral proteins'

Links tagged with 'viral proteins'

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Found 11 links

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AD-ENMTool Content

http://enm.lobos.nih.gov [open in a new window]

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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.

links directory index: 256
TitlePublication YearGoogle Scholar Citation Count
Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin200545
Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved200552
Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model200559
A comparative study of motor-protein motions by using a simple elastic-network model2003100
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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

ELMTool Content

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

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Eukaryotic Linear Motif (ELM) resource is a tool for predicting eukaryotic protein functional sites that report domains, motifs, and sequence patterns based on the input sequence.

links directory index: 1035
TitlePublication YearGoogle Scholar Citation Count
ELM--the database of eukaryotic linear motifs201215
ELM: the status of the 2010 eukaryotic linear motif resource201090
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins2003465
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins2003465
NAR Database Issue 2010NAR Web Server Issue 2003
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external linksLink on Wikipedia
tagsamino acid motifs amino acid sequence amino acid sequence homology animals computational biology computer graphics disease eukaryota eukaryotic cells genetic databases humans information storage and retrieval internet molecular sequence data nucleic acid databases protein databases protein sequence analysis proteins software tertiary protein structure user-computer interface viral proteins

FluGenomeTool Content

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

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

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

links directory index: 41
TitlePublication YearGoogle Scholar Citation Count
FluGenome: a web tool for genotyping influenza A virus200741
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 [open in a new window]

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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.

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
GWIDD: Genome-wide protein docking database201011
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

PhEVERDatabase Content

http://pbil.univ-lyon1.fr/databases/phever [open in a new window]

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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.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
PhEVER: a database for the global exploration of virus-host evolutionary relationships20111
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/ [open in a new window]

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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.

links directory index: 10
TitlePublication YearGoogle Scholar Citation Count
PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery200810
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/ [open in a new window]

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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.

links directory index: 318
TitlePublication YearGoogle Scholar Citation Count
ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition200628
Intermolecular and intramolecular readout mechanisms in protein-DNA recognition200487
Specificity of protein-DNA recognition revealed by structure-based potentials: symmetric/asymmetric and cognate/non-cognate binding200262
Structure-based prediction of DNA target sites by regulatory proteins1999141
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/ [open in a new window]

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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.

links directory index: 59
TitlePublication YearGoogle Scholar Citation Count
Prediction of lipid posttranslational modifications and localization signals from protein sequences: big-Pi, NMT and PTS1200359
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 [open in a new window]

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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.

links directory index: 326
TitlePublication YearGoogle Scholar Citation Count
TROD: T7 RNAi Oligo Designer200416
RNA interference in mammalian cells using siRNAs synthesized with T7 RNA polymerase2002310
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

ViralZoneDatabase Content

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

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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.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
ViralZone: a knowledge resource to understand virus diversity20112
NAR Database Issue 2011
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external linksLink on Wikipedia
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 [open in a new window]

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Model Organisms > Microbes
Protein > Networks & Interactions, Pathways and 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.

links directory index: 30
TitlePublication YearGoogle Scholar Citation Count
VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks200930
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tagshost-pathogen interactions protein databases protein interaction mapping proteome viral proteins virus diseases virus physiological phenomena

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