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Links tagged with 'escherichia coli proteins'

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BioCyc Knowledge LibraryDatabase Content

http://www.biocyc.org/

Protein > Interactions, Pathways, Enzymes

BioCyc is a collection of pathway/genome databases derived either from the literature (EcoCyc and MetaCyc) or computationally (ie. HumanCyc). EcoCyc is used to visualize gene layout, biochemical reactions, and pathways for the E. coli chromosome; MetaCyc contains the enzymes, reactions, and pathways for a variety of organisms (mostly micro-organisms)

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tagsbacterial gene expression regulation bacterial genome database management systems enzymes escherichia coli escherichia coli proteins genetic databases genome humans metabolism protein databases protein transport signal transduction

CaspRTool Content

http://igs-server.cnrs-mrs.fr/Caspr/index.cgi

Protein > 3-D Structure Prediction

CaspR is a web tool for building structural models for protein sequences using molecular replacement and homology modelling. The software implements an automated approach that uses T-COFFEE to produce alignments, MODELLER to produce homology models, and finally uses AMoRe and CNS to produce the structural model.

NAR Web Server Issue 2004
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tagsescherichia coli proteins molecular models protein sequence analysis protein structural homology sequence alignment

EcoCycDatabase Content

http://EcoCyc.org

Model Organisms > Databases

EcoCyc is a comprehensive model organism database for Escherichia coli K-12 MG1655. From the scientific literature, EcoCyc captures the functions of individual E. coli gene products; their regulation at the transcriptional, post-transcriptional and protein level; and their organization into operons, complexes and pathways. EcoCyc users can search and browse the information in multiple ways. New features include combined gene/protein pages and a Regulation Summary Diagram displaying a graphical overview of all known regulatory inputs to gene expression and protein activity.

NAR Database Issue 2011
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tagsbacterial gene expression regulation binding sites escherichia coli k12 escherichia coli proteins genetic databases genetic transcription signal transduction transcription factors

HHompTool Content

http://toolkit.tuebingen.mpg.de/hhomp

DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Model Organisms > Microbes

HHomp is a web server for prediction and classification of outer membrane proteins (OMPs). Beginning with sequence similarity of a protein to known OMPs, HHomp builds a hidden markov model (HMM) and compares the input sequence to a database of OMPs by pairwise HMM comparison. The OMP database contains profile HMMs for over 20,000 putative OMP sequences.

This content is being maintained by mremmert.

NAR Web Server Issue 2009
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tagsamino acid sequence homology bacterial outer membrane proteins escherichia coli proteins protein databases

NOMAD-RefTool Content

http://lorentz.immstr.pasteur.fr/nomad-ref.php

Protein > Molecular Dynamics and Docking

Normal Mode Analysis, Deformation, and Refinement (NOMAD-Ref) provides tools for calculating functionally relevant movements in biological macromolecules. This resource provides tools for investigating different conformations of large protein structures, for modeling receptor/ligand docking complexes, and for calculating the associated molecular motions.

NAR Web Server Issue 2006
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tagscarrier proteins computer simulation dna dna-binding proteins dna-directed dna polymerase dna-directed rna polymerases escherichia coli proteins ligands macromolecular substances mathematical computing molecular models molecular structure motion neural networks (computer) protein conformation proteins x-ray diffraction

Pathway Hunter ToolTool Content

http://pht.tu-bs.de/PHT/

Protein > Interactions, Pathways, Enzymes

Pathway Hunter Tool (PHT) uses shortest path analysis to reconstruct and visualize biochemical pathways. The user can find the shortest path between two metabolites, or find all reachable products or educts for a given metabolite.

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tagsalgorithms biological models computer simulation energy metabolism escherichia coli escherichia coli proteins factual databases gene expression profiling gene expression regulation protein interaction mapping signal transduction transcription factors

Phydbac2Tool Content

http://igs-server.cnrs-mrs.fr/phydbac/

Model Organisms > Microbes
Protein > Annotation and Function
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics

Phydbac2 (Phylogenomic display of bacterial genes) is a tool to visualize and explore the phylogenomic profiles of bacterial protein sequences. It also allows the user to view sequence similarity across different organisms, access other genes with similar conservation profiles, and view genes that are found nearby a selected gene in multiple genomes.

NAR Web Server Issue 2004NAR Web Server Issue 2003
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tagsartificial gene fusion bacterial chromosomes bacterial genes bacterial genome bacterial proteins chromosome mapping escherichia coli proteins genomics molecular evolution open reading frames phylogeny protein sequence analysis

PRED-TMBBTool Content

http://bioinformatics.biol.uoa.gr/PRED-TMBB/

Protein > 2-D Structure Prediction
Protein > Localization and Targeting

PRED-TMBB is a tool that takes a Gram-negative bacteria protein sequence as input and predicts the transmembrane strands and the probability of it being an outer membrane beta-barrel protein. The user has a choice of three different decoding methods.

This content is being maintained by pbagos.

NAR Web Server Issue 2004
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tagsbacterial outer membrane proteins escherichia coli proteins gram-negative bacteria hidden markov model markov chains membrane proteins peptides predictive value of tests protein databases protein sequence analysis secondary protein structure statistical models tertiary protein structure topology prediction

REPAIRtoireDatabase Content

http://repairtoire.genesilico.pl/

Protein > Databases

REPAIRtoire is a database resource for systems biology of DNA damage and repair. The database collects and organizes the following types of information: (i) DNA damage linked to environmental mutagenic and cytotoxic agents, (ii) pathways comprising individual processes and enzymatic reactions involved in the removal of damage, (iii) proteins participating in DNA repair and (iv) diseases correlated with mutations in genes encoding DNA repair proteins. REPAIRtoire also provides links to publications and external databases. REPAIRtoire contains information about eight main DNA damage checkpoint, repair and tolerance pathways: DNA damage signaling, direct reversal repair, base excision repair, nucleotide excision repair, mismatch repair, homologous recombination repair, nonhomologous end-joining and translesion synthesis. The pathway/protein dataset is currently limited to three model organisms: Escherichia coli, Saccharomyces cerevisiae and Homo sapiens. The DNA repair and tolerance pathways are represented as graphs and in tabular form with descriptions of each repair step and corresponding proteins, and individual entries are cross-referenced to supporting literature and primary databases. REPAIRtoire can be queried by the name of pathway, protein, enzymatic complex, damage and disease.

This content is being maintained by iamb@genesilico.pl.

NAR Database Issue 2011
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tagsdisease dna damage dna repair dna repair enzymes escherichia coli proteins humans mutagens mutation protein databases saccharomyces cerevisiae proteins

SIFTTool Content

http://blocks.fhcrc.org/sift/SIFT.html

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms
Protein > Annotation and Function

Sorting Intolerant From Tolerant (SIFT) is a sequence homology-based tool that will predict whether an amino acid substitution will affect protein function.

NAR Web Server Issue 2003
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tagsamino acid motifs amino acid sequence amino acid substitution bacterial proteins bacteriophage t4 chromosome mapping computational biology conserved sequence dna sequence analysis escherichia coli proteins false positive reactions genes genetic polymorphism hiv protease hiv-1 humans inborn genetic diseases lac repressors lactose missense mutation molecular sequence data muramidase mutation phenotype probability protein databases protein sequence analysis proteins pseudogenes repressor proteins sequence alignment single nucleotide polymorphism

taveRNATool Content

http://compbio.cs.sfu.ca/taverna/

RNA > Functional RNAs
RNA > Structure Prediction, Visualization, and Design

taveRNA hosts three RNA web services: alteRNA, inteRNA and pRuNA. alteRNA is an alternative to many RNA folding methods. inteRNA predicts the joint secondary structure of two RNA sequences. pRuNA is an database pruning method which given a query RNA returns only a few ncRNAs as potential regulators.

NAR Web Server Issue 2007
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tagsadenosine triphosphatases algorithms antisense rna bacterial genome bacterial rna base sequence binding sites cation transport proteins chemical models computational biology computer simulation escherichia coli escherichia coli proteins humans molecular sequence data nucleic acid conformation plasmids programming languages rna rna sequence analysis rna stability sequence alignment statistical models trans-activators

The Protein OntologyDatabase Content

http://pir.georgetown.edu/pro

Protein > Databases

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein research.

NAR Database Issue 2011
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tagsanimals controlled vocabulary escherichia coli proteins humans mice multiprotein complexes protein databases protein isoforms proteins