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Links tagged with 'bacterial proteins'

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3D-FootprintDatabase Content

http://floresta.eead.csic.es/3dfootprint

DNA > Databases
Protein > Databases

3D-footprint provides estimates of binding specificity for all protein-DNA complexes available at the Protein Data Bank. The web interface allows the user to: (i) browse DNA-binding proteins by keyword; (ii) find proteins that recognize a similar DNA motif and (iii) BLAST similar DNA-binding proteins, highlighting interface residues in the resulting alignments. Comparisons with expert-curated databases RegulonDB and TRANSFAC support the quality of structure-based estimates of specificity.

This content is being maintained by brunocontreras.

NAR Database Issue 2010
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tagsanimals bacterial proteins computational biology dna-binding proteins genetic databases genetic regulation humans nucleic acid databases protein conformation protein databases protein-DNA complex pubmed regulator genes sequence alignment

3D-pssmTool Content

http://www.sbg.bio.ic.ac.uk/~3dpssm/index2.html

Protein > 3-D Structure Prediction

Protein fold recognition using 1d and 3d sequence profiles coupled with secondary structure and solvation potential information.

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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial genome bacterial proteins computational biology factual databases flavoproteins integrases molecular models molecular sequence data mycoplasma open reading frames protein folding proteins proteome reproducibility of results retroviridae proteins ribonuclease h secondary protein structure sequence alignment solvents structure-activity relationship

Andrej Sali LabResource Content

http://salilab.org/our_resources.shtml

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Molecular Dynamics and Docking

This page contains various resources for comparative protein structure modelling and analysis from the Sali Lab at University of California at San Francisco (UCSF).

NAR Web Server Issue 2003
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tagsamino acid sequence amino acid sequence homology animals bacterial proteins carrier proteins l-lactate dehydrogenase molecular models molecular sequence data protein databases protein folding protein structural homology proteins reproducibility of results sequence alignment sequence homology systems integration tertiary protein structure trichomonas vaginalis

BROPResource Content

http://brop.org/

Expression > Transcript Expression Analysis
Model Organisms > Microbes

The Bioinformatics Resource for Oral Pathogens (BROP) contains tools for genomics of oral pathogens including Genome Viewer, GOAL (genome wide ORF alignment), an oral pathogen microarray database, an entrez counter, oral pathogen specific BLAST, and a codon usage database.

NAR Web Server Issue 2005
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tagsbacteria bacterial capsules bacterial genes bacterial genome bacterial polysaccharides bacterial proteins biological evolution computational biology dna transposable elements fungal genome genetic databases genetic variation genomic islands genomics horizontal gene transfer integrases mouth oligonucleotide array sequence analysis open reading frames operon porphyromonas gingivalis sequence alignment streptococcus mutans transfer rna virulence virulence factors

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

COGsTool Content

http://www.ncbi.nlm.nih.gov/COG/

Protein > Domains and Motifs
Sequence Comparison > Comparative Genomics

Clusters of Orthologous Groups represent ancient conserved protein domains; use COGnitor tool to find COGS in sequence of interest.

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tagsamino acid sequence animals archaea archaeal genes archaeal proteins bacteria bacterial genes bacterial proteins caenorhabditis elegans conserved sequence drosophila melanogaster factual databases fungal genes fungal proteins genome methanococcus molecular evolution multigene family phylogeny proteins saccharomyces cerevisiae sequence alignment species specificity

ComSinDatabase Content

http://antares.protres.ru/comsin/.

Protein > Databases

ComSin is a database of protein structures in bound (complex) and unbound (single) states. The developed server enables one to search for proteins in bound and unbound states with several options including sequence similarity between the corresponding proteins in bound and unbound states, and validation of interaction interfaces of protein complexes.

NAR Database Issue 2010
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tagsanimals bacterial proteins computational biology genetic databases humans molecular conformation molecular models protein binding protein conformation protein databases tertiary protein structure

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

Dali serverDatabase Content

http://ekhidna.biocenter.helsinki.fi/dali_server

Protein > 3-D Structure Comparison

The Dali server compares newly solved structures against structures in the PDB, allows browsing of pre-computed structural neighborhoods and generates suboptimal alignments from pairwise structure comparisons.

NAR Web Server Issue 2010
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tagsbacterial proteins protein databases protein sequence analysis protein structural homology

DIPDatabase Content

http://dip.doe-mbi.ucla.edu/

Protein > Interactions, Pathways, Enzymes

The Database of Interacting Proteins (DIP) allows users to search for interacting proteins. Results lists can be searched and/or visualized (statically or dynamically). Users can submit new protein-protein interactions and update database entries.

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tagsanimals bacterial proteins computational biology factual databases forecasting fungal proteins helicobacter pylori humans information services macromolecular substances molecular models precipitin tests protein binding protein databases proteins reproducibility of results tertiary protein structure two-hybrid system techniques

EffectiveDatabase Content

http://effectors.org

Protein > Databases

Effective is a database of predicted bacterial secreted proteins, implementing two complementary prediction strategies for protein secretion: the identification of eukaryotic-like protein domains and the recognition of signal peptides in amino acid sequences. The Effective web portal provides user-friendly tools for browsing and retrieving comprehensive precalculated predictions for whole bacterial genomes as well as for the interactive prediction of effectors in user-provided protein sequences.

NAR Database Issue 2011
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tagsbacterial genome bacterial proteins protein databases protein sorting signals tertiary protein structure

fPOPDatabase Content

http://pocket.uchicago.edu/fpop/

Protein > Databases

fPOP (footprinting Pockets Of Proteins) is a relational database of the protein functional surfaces identified by analyzing the shapes of binding sites in approximately 42,700 structures, including both holo and apo forms. To identify protein binding sites, we model the shape of a split pocket induced by a binding ligand(s). This database provides an easily accessible resource for studying functional surfaces, assessing conformational changes between bound and unbound forms and analyzing functional divergence. The database facilitates the exploration of the physicochemical textures of molecules and the inference of protein function and provides a framework for classification of proteins into families on the basis of their functional surfaces.

NAR Database Issue 2010
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tagsalgorithms animals bacterial proteins binding sites computational biology computer simulation genetic databases humans protein conformation protein databases proteins tertiary protein structure

GDAPTool Content

http://www.doe-mbi.ucla.edu/Services/GDAP

Protein > Biochemical Features
Protein > Sequence Features

The Genomic Disulfide Analysis Program (GDAP) predicts disulfide bonds for a user-supplied protein sequence. GDAP also provides access to pre-computed predictions of disulfide bonds for over 100 microbial genomes.

NAR Web Server Issue 2004
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tagsarchaeal genome archaeal proteins bacterial genome bacterial proteins cysteine disulfides protein sequence analysis statistical data interpretation

GeConT 2Tool Content

http://gecont.ibt.unam.mx/cgi-bin/gecont/gecont.pl

DNA > Sequence Retrieval and Submission
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

The Gene Context Tool (GeConT) is a visualization tool for viewing the genomic context of a gene or group of genes, and their orthologous relationships, within any of the fully sequenced bacterial genomes. Sequence retrieval is also possible.

NAR Web Server Issue 2008
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tagsbacteria bacterial genes bacterial genome bacterial proteins conserved sequence genomics tertiary protein structure

HHpredTool Content

http://protevo.eb.tuebingen.mpg.de/hhpred

Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Sequence Comparison > Similarity Searching

Based on the comparison of profile HMMs, HHpred takes a protein sequence or multiple sequence alignment as input and searches for remote homologues in an assortment of databases such as PDB, SMART and Pfam. The user can select either a local or global alignment method, and the search results can be used to generate 3D structural models.

NAR Web Server Issue 2005
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tagsamino acid sequence homology bacterial proteins markov chains protein conformation protein databases protein sequence analysis sequence alignment transcription factors