А кроме того - Новосибирской школе биологии опубликовавшей список групп и баз данных, относящихся к биоинформатике.
Молекулярно-генетический сервер
(
http://wwwmgs.bionet.nsc.ru/mgs/)
E-cell (
http://www.e-cell.org;http://ecell.sourceforge.net/;http://www.bioinfo.sfc.keio.ac.jp/)
CyberCell
(
http://redpoll.pharmacy.ualberta.ca/CCDB/)
SiliconCell (
http://www.bio.vu.nl/hwconf/Silicon/index.html)
Systems Biology Research Group
(
http://gcrg.ucsd.edu/)
Arkin Laboratory for Dynamical Genomics
(
http://gobi.lbl.gov/)
Kitano Symbiotic Systems Project, ERATO,
JST (
http://www.symbio.jst.go.jp;http://www.sbw-sbml.org)
VTT Biotechnology (
http://sysbio.vtt.fi/)
Biosystems Group at UCSF
(
http://biosystems.ucsf.edu/)
Institute for Systems Biology
(
http://www.systemsbiology.org/)
Systems Biology Resource
(
http://www.systems-biology.org/)
PNNL: The Pacific Northwest National Laboratory
(
http://www.sysbio.org/)
YSBN: The Yeast Systems Biology Network
(
http://ysbn.org)
NRCAM: The National Resource for Cell
Analysis and Modeling
(
http://www.nrcam.uchc.edu/)
Gene Network Inference from Large-Scale
Gene Expression Data Resource
(
http://www.cs.unm.edu/~patrik/networks/networks.html)
Plant Systems Biology Resource
(
http://www.psb.rug.ac.be/)
Cellular Networks at Notre Dame
(
http://www.nd.edu/~networks/cell/)
BioPathways Consortium
(
http://www.biopathways.org/)
EMC2: E. coli Model Cell Consortium
(
http://ecmc2.sdsc.edu/)
SBML: The Systems Biology Markup Language
(
http://www.sbml.org/)
CellML (
http://www.cellml.org/)
Genomatica (
http://www.genomatica.com/)
Cellnomatica (
http://www.cellnomica.com/)
Gene Networks Sciences
(
http://www.gnsbiotech.com/)
Physiome Sciences
(
http://www.physiome.com/)
Entelos (
http://www.entelos.com/)
Languages for Systems Biology (http://
www.luca.demon.co.uk/BioComputing.htm)
Bio-IT World – Resource and Articles on
Systems Biology (
http://www.bio-itworld.com/resources/systems/)
Приложение 3
Базы данных по регуляторным путям:
GeneNet: Gene Networks Database
(
http://www.sgi.sscc.ru/mgs/gnw/genenet/)
KEGG: Regulatory Pathways (http://
www.genome.ad.jp/kegg/regulation.html)
SPAD: Signal Transduction
(
http://www.grt.kyushu-u.ac.jp/spad/)
CSNDB: Cell Signaling Networks
(
http://geo.nihs.go.jp/csndb/)
MIPS: Yeast Pathways (
http://www.mips.biochem.
mpg.de/proj/yeast/pathways/index.html)
Вестник ВОГиС, 2005, Том 9, № 2 255
Interactive Fly: Drosophila Genes (http://
sdb.bio.purdue.edu/fly/aimain/1aahome.htm)
GeNet: Gene Networks Database
(
http://www.csa.ru/Inst/gorb_dep/inbios/genet/genet.htm)
HOX-Pro: Homeobox Genes Database
(
http://www.iephb.nw.ru/labs/lab38/spirov/hox_pro/hox-pro00.html)
Wnt Signaling Pathway (http://
www.stanford.edu/~rnusse/wntwindow.html)
TRANSPATH: Gene Regulatory Pathways
(
http://transpath.gbf.de/)
Базы данных по метаболическим путям:
KEGG: Metabolic Pathways (http://
www.genome.ad.jp/kegg/metabolism.html)
EMP: Enzymes and Metabolic Pathways
(
http://emp.mcs.anl.gov/)
WIT: Metabolic Reconstruction
(
http://wit.mcs.anl.gov/WIT2/)
UM-BBD: Microbial Biocatalysis/
Biodegradatation (
http://umbbd.ahc.umn.edu/)
BioCyc: Procariotic Genes and Metabolism
(
http://biocyc.org/)
EcoCyc: E. coli Genes and Metabolism
(
http://ecocyc.org/)
HumanCyc: Homo sapiens Genes and Metabolism
(
http://humancyc.org/)
MetaCyc: Metabolism from 150 species
(
http://metacyc.org/)
SoyBase: Soybean Metabolism
(
http://cgsc.biology.yale.edu/metab.htm)
Metalgen: Genes and Metabolism
(
http://indigo.genetique.uvsq.fr/)
Boehringer Mannheim: Biochemical Pathways
(
http://www.expasy.ch/cgi-bin/searchbiochem-index)
IUBMB-Nicholson Minimaps (http://
www.tcd.ie/Biochemistry/IUBMB-Nicholson/)
Базы данных по ферментам, низкомолеку-
лярным веществам и реакциям:
LIGAND: Biochemical Compounds and Reactions
(
http://www.genome.ad.jp/ligand/)
ENZYME: Enzymes (
http://www.expasy.ch/enzyme/)
BRENDA: Comprehensive Enzyme Information
System (
http://www.brenda.uni-koeln.de/)
Worthington Enzyme Manual
(
http://www.worthington-biochem.com/manual/manIndex.html)
Klotho: Biochemical Compounds
(
http://www.biocheminfo.org/klotho/)
ChemFinder: Searching Chemicals
(
http://chemfinder.camsoft.com/)
ChemIDplus at NLM
(
http://chem.sis.nlm.nih.gov/chemidplus/)
PROMISE: Prosthetic Groups and Metal Ions
(
http://metallo.scripps.edu/PROMISE/)
GlycoSuiteDB: Glycan Structure Database
(
http://www.glycosuite.com/)
CarbBank: Complex Carbohydrate Structure
Database (
http://bssv01.lancs.ac.uk/gig/pages/gag/carbbank.htm)
LIPIDBANK: for Web - Lipids
(
http://lipidbank.jp/)
WebElements: Periodic Table
(
http://www.webelements.com/)
PDB: Protein Data Bank (
http://www.rcsb.org/pdb/)
Базы данных по белок-белковым взаимодей-
ствиям:
BRITE: Database for Biomolecular Relations
(
http://www.genome.ad.jp/brite/)
DIP: Database of Interacting Proteins
(
http://dip.doe-mbi.ucla.edu/)
BIND: Biomolecular Interaction Network Database
(
http://www.binddb.org/)
Базы данных по транскрипционным
факторам:
TRRD: Transcription Regulatory Regions Database
(
http://www.sgi.sscc.ru/mgs/gnw/trrd/)
TRANSFAC: Transcription Factor Database
(
http://transfac.gbf.de/TRANSFAC/index.html)
RegulonDB: E. coli Transcriptional Regulation
(
http://www.cifn.unam.mx/Computational_Genomics/regulondb)
DBTBS: B. subtilis Transcription Factors
(
http://elmo.ims.u-tokyo.ac.jp/dbtbs/)
SCPD: S. cerevisiae Promoter Database
(
http://cgsigma.cshl.org/jian/)
DPInteract: DNA binding proteins
(
http://arep.med.harvard.edu/dpinteract/)
Базы данных по паттернам экспрессии генов:
Axeldb: Xenopus laevis (
http://www.dkfzheidelberg.
de/abt0135/axeldb.htm)
NEXTDB: Caenorhabditis elegans
(
http://nematode.lab.nig.ac.jp/)
MAGEST: Halocynthia roretzi
(
http://www.genome.ad.jp/magest/)