> Tag > Links tagged with 'biological models'

Links tagged with 'biological models'

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Found 36 links

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ADGOTool Content

http://www.btool.org/ADGO2 [open in a new window]

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Expression > Gene Set Analysis
Expression > cDNA, EST, SAGE

ADGO is a web tool that provides composite interpretations for microarray data comparing two sample groups. It also provides composite interpretations and enrichment analysis for lists of genes from diverse sources of biological information.

links directory index: 28
TitlePublication YearGoogle Scholar Citation Count
ADGO 2.0: interpreting microarray data and list of genes using composite annotations.20113
ADGO: analysis of differentially expressed gene sets using composite GO annotation200625
NAR Web Server Issue 2011
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tagsalgorithms animals biological models cell differentiation computer simulation documentation gene expression profiling genes humans mice molecular sequence annotation oligonucleotide array sequence analysis protein databases proteins rats t-lymphocytes

ASIANTool Content

http://eureka.cbrc.jp/asian/ [open in a new window]

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Expression > Transcript Expression Analysis

ASIAN (Automatic System for Inferring a Network) is a server for inferring regulatory networks from gene expression profiles that combines cluster analysis, regression analysis, and graphical Gaussian modeling.

links directory index: 287
TitlePublication YearGoogle Scholar Citation Count
ASIAN: a web server for inferring a regulatory network framework from gene expression profiles200523
ASIAN: a website for network inference200417
Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling2002186
Statistical estimation of cluster boundaries in gene expression profile data200161
NAR Web Server Issue 2005
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tagsanalysis of variance bayes theorem biological models cluster analysis computational biology computer simulation factual databases fungal genes gene expression gene expression profiling gene expression regulation genetic models oligonucleotide array sequence analysis proteome regression analysis saccharomyces cerevisiae signal transduction statistical data interpretation statistical models

BiologicalNetworksTool Content

http://brak.sdsc.edu/pub/BiologicalNetworks/ [open in a new window]

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Expression > Transcript Expression Analysis
Protein > Networks & Interactions, Pathways and Enzymes

BiologicalNetworks allows retrieval, construction, and visualization of biological networks and allows for the analysis of high-throughput expression data by mapping onto network graphs. BiologicalNetworks queries the PathSys system, a combined database of biological pathways, gene regulatory networks, and protein interaction maps.

links directory index: 64
TitlePublication YearGoogle Scholar Citation Count
BiologicalNetworks: visualization and analysis tool for systems biology200664
PathSys: integrating molecular interaction graphs for systems biology.20060
NAR Web Server Issue 2006
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tagsbiological models computer simulation gene expression profiling genetic databases genomics oligonucleotide array sequence analysis protein databases protein interaction mapping saccharomyces cerevisiae proteins signal transduction systems biology systems integration

BioNumbersDatabase Content

http://www.bionumbers.hms.harvard.edu [open in a new window]

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Literature > Databases

BioNumbers (http://www.bionumbers.hms.harvard.edu) is a database of key numbers in molecular and cell biology--the quantitative properties of biological systems of interest to computational, systems and molecular cell biologists. Contents of the database range from cell sizes to metabolite concentrations, from reaction rates to generation times, from genome sizes to the number of mitochondria in a cell. All numbers are taken directly from a literature source and that reference is provided with the number.

links directory index: 20
TitlePublication YearGoogle Scholar Citation Count
BioNumbers--the database of key numbers in molecular and cell biology201020
NAR Database Issue 2010
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tagsalgorithms animals biological models cell biology computational biology genetic databases humans molecular biology nucleic acid databases protein databases systems biology theoretical models

BioverseTool Content

http://bioverse.compbio.washington.edu/ [open in a new window]

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DNA > Annotations
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Annotation and Function
Protein > Sequence Comparison
Protein > Sequence Retrieval

Bioverse is a system that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information.

links directory index: 95
TitlePublication YearGoogle Scholar Citation Count
Functional annotation from predicted protein interaction networks200537
BIOVERSE: enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes200513
Enhanced functional information from predicted protein networks200420
Bioverse: Functional, structural and contextual annotation of proteins and proteomes200325
NAR Web Server Issue 2005NAR Web Server Issue 2003
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tagsamino acid sequence homology biological models chromosome mapping computer simulation energy metabolism gene expression profiling gene expression regulation molecular models protein conformation protein interaction mapping protein sequence analysis proteins proteome proteomics signal transduction

CDDDatabase Content

http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml [open in a new window]

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Protein > Databases

NCBI's Conserved Domain Database (CDD) is a resource for the annotation of protein sequences with the location of conserved domain footprints, and functional sites inferred from these footprints. CDD includes manually curated domain models that make use of protein 3D structure to refine domain models and provide insights into sequence/structure/function relationships.

This content is being maintained by Aron Marchler-Bauer.

links directory index: 208
TitlePublication YearGoogle Scholar Citation Count
CDD: a Conserved Domain Database for the functional annotation of proteins2011208
NAR Database Issue 2011
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external linksLink on Wikipedia
tagsamino acid sequence biological models conserved sequence protein databases protein sequence analysis proteins tertiary protein structure

Cell++Tool Content

http://sourceforge.net/projects/cellpp/ [open in a new window]

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Protein > 3-D Structure Retrieval/Viewing
Protein > Biochemical Features
Protein > Networks & Interactions, Pathways and Enzymes

Cell++ is a novel stochastic simulation environment which is capable of modelling diverse biochemical phenomena including signal transduction pathways, metabolic pathways and intracellular calcium signalling.

links directory index: 19
TitlePublication YearGoogle Scholar Citation Count
Cell++--simulating biochemical pathways200619
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tagsbiochemistry biological models cell physiological phenomena computer simulation programming languages proteome signal transduction
setsUniversity of Toronto

ClusProTool Content

http://cluspro.bu.edu/login.php [open in a new window]

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Protein > Molecular Dynamics and Docking

ClusPro is a tool for automatically computing the docking of two protein structures supplied by the user (or as PDB IDs). The result set is a ranked list of putative complexes, ordered by clustering properties.

links directory index: 511
TitlePublication YearGoogle Scholar Citation Count
Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19201033
PIPER: an FFT-based protein docking program with pairwise potentials2006100
ClusPro: an automated docking and discrimination method for the prediction of protein complexes2004247
ClusPro: a fully automated algorithm for protein-protein docking2004131
NAR Web Server Issue 2004
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tagsalgorithms antibodies antigens binding sites biological models chemical models cluster analysis computational biology discriminant analysis energy transfer enzyme inhibitors fourier analysis molecular dynamics simulation molecular models monte carlo method protein binding protein conformation protein interaction mapping protein multimerization proteins reproducibility of results sensitivity and specificity static electricity time factors

eF-seekTool Content

http://ef-site.hgc.jp/eF-seek/index.jsp [open in a new window]

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Protein > 3-D Structural Features
Protein > 3-D Structure Comparison

eF-seek predicts protein functional sites by searching for similar electrostatic potential and molecular surface shapes against eF-site, a database of electrostatic surfaces for representative ligand binding sites.

This content is being maintained by Kenta Nakai.

links directory index: 409
TitlePublication YearGoogle Scholar Citation Count
eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape200727
Identification of the ligand binding sites on the molecular surface of proteins200547
eF-site and PDBjViewer: database and viewer for protein functional sites200472
Identification of protein biochemical functions by similarity search using the molecular surface database eF-site2003118
Protein informatics towards function identification200352
Identification of protein functions from a molecular surface database, eF-site200293
NAR Web Server Issue 2007
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tagsalgorithms antibodies binding sites biological models computational biology computer simulation database management systems ligands molecular models protein conformation protein databases protein folding proteins proteomics s-adenosylhomocysteine static electricity structure-activity relationship three-dimensional imaging trypsin

GeneProTool Content

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

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Protein > Networks & Interactions, Pathways and Enzymes

A Cytoscape plug-in for advanced visualization and analysis of interaction networks.

This content is being maintained by shoshana Wodak.

links directory index: 34
TitlePublication YearGoogle Scholar Citation Count
GenePro: a Cytoscape plug-in for advanced visualization and analysis of interaction networks200634
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tagsalgorithms biological models computer simulation computing methodologies gene expression profiling oligonucleotide array sequence analysis protein interaction mapping proteome signal transduction
setsUniversity of Toronto

GenomeNetTool Content

http://www.genome.ad.jp/ [open in a new window]

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DNA > Sequence Retrieval and Submission
Human Genome > Other Resources
Protein > Networks & Interactions, Pathways and Enzymes
Protein > Sequence Retrieval

Network of database and computational resources including KEGG (pathways, interactions, etc.) and DBGET/LinkDB (an integrated database retrieval system). It also hosts several web-based tools for sequence analysis (ie. Blast, Motif, Clustal W)

links directory index: 285
TitlePublication YearGoogle Scholar Citation Count
The KEGG database2002182
DBGET/LinkDB: an integrated database retrieval system1998103
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tagsamino acid sequence animals biological models computer simulation factual databases genetic models genome humans information systems japan ligands molecular biology molecular sequence data protein binding proteome

KEGG: Kyoto Encyclopedia of Genes and GenomesDatabase Content

http://www.genome.ad.jp/kegg/ [open in a new window]

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Expression > Networks
Protein > Networks & Interactions, Pathways and Enzymes
Protein > Proteomics

Pathway maps, molecular catalogs, genome maps and gene catalogs that capture knowledge about interactions in terms of information pathways. KEGG comprises several databases, including BRITE (protein-protein interactions), PATHWAY (interaction networks for cellular processes), and LIGAND (chemical compounds and chemical reactions). KEGG Atlas is a new tool for the global analysis of metabolic pathways.

links directory index: 5191
TitlePublication YearGoogle Scholar Citation Count
KEGG for linking genomes to life and the environment20081156
KEGG Atlas mapping for global analysis of metabolic pathways2008146
The KEGG database2002182
KEGG: Kyoto Encyclopedia of Genes and Genomes19993707
NAR Web Server Issue 2008
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tagsamino acid sequence animals biological models computational biology computer simulation disease factual databases gene expression genes genetic models genome genomics humans japan ligands metabolic networks and pathways metabolism molecular sequence data molecular structure pharmaceutical preparations protein binding proteome sequence homology systems biology systems integration

KOBASTool Content

http://kobas.cbi.pku.edu.cn [open in a new window]

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DNA > Annotations
Human Genome > Databases
Protein > Networks & Interactions, Pathways and Enzymes

KEGG Orthology-Based Annotation System (KOBAS) annotates sequences with KEGG Orthology terms and identifies the frequently occurring (or significantly enriched) pathways among the queried sequences compared against a background distribution. 5 pathway databases are used (KEGG Pathway, PID, BioCyc, Reactome, Panther) and 5 human databases (OMIM, KEGG Disease, FunDO, GAD, NHGRI GWAS).

links directory index: 215
TitlePublication YearGoogle Scholar Citation Count
KOBAS server: a web-based platform for automated annotation and pathway identification200675
Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary2005140
NAR Web Server Issue 2006NAR Web Server Issue 2011
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tagsalzheimer disease artificial intelligence biological models chromosome mapping controlled vocabulary database management systems documentation genes genetic databases hippocampus natural language processing proteins proteome sequence analysis signal transduction statistical data interpretation up-regulation

M4TTool Content

http://manaslu.aecom.yu.edu/M4T/ [open in a new window]

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Protein > 3-D Structure Prediction

M4T (Multiple Mapping Method with Multiple Templates) is a comparative protein structure modeling server that uses a combination of multiple templates and iterative optimization of alternative alignments.

links directory index: 26
TitlePublication YearGoogle Scholar Citation Count
M4T: a comparative protein structure modeling server200726
NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence biological models computational biology computer simulation molecular models molecular sequence data protein sequence analysis proteins secondary protein structure sequence alignment theoretical models

MetaCycDatabase Content

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

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Protein > Databases

The MetaCyc database is a comprehensive resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. Pathways reactions are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes, and literature citations.

links directory index: 493
TitlePublication YearGoogle Scholar Citation Count
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.201236
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases2010457
NAR Database Issue 2010
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external linksLink on Wikipedia
tagsanimals archaeal genome bacterial genome biological models computational biology genetic databases humans nucleic acid databases plant genome protein databases tertiary protein structure viral genome

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