分子生物数据库

一。核酸及其相关数据库

1.核酸序列数据库

BIOSINO 我国的核酸序列公共数据库
EMBL - EMBL Nucleotide sequence database (EBI) *
GenBank - GenBank Nucleotide Sequence database (NCBI) *
DDBJ - DNA Data Bank of Japan *
dbEST - Database of Expressed Sequence Tags (NCBI)
dbSTS - Database of Sequence Tagged Sites (NCBI) 　
2.基因组及相关数据库 Genomic Databases

GenomeWeb(HGMP) - A catalogue of useful Web sites for Genomics with a set of collections of genome databases
GSDB - Genome Sequence database (NCGR)
GOLD - Genomes On-line db
一些数据库的直接链接
DOGS - Database of Genome Sizes
Genomics web site (John Wiley & Sons Ltd) (The Genomics website at Wiley is a new and DYNAMIC resource for the genomics community, offering FREE special feature articles and new information EACH MONTH.)
HUGO - HUman Genome Organization　
3.核酸三维结构数据库

NDB - Nucleic Acid Databank (3D structures)
BNASDB - Nucleic acid structure db from University of Pune 　
4 转基因数据库（Transgenics）

Cre Transgenic Database - Cre transgenic mouse lines
Transgenic/Targeted Mutation Database - Information on transgenic animals and targeted mutations
5.其他

AsDb - Aberrant Splicing db
ACUTS - Ancient conserved untranslated DNA sequences db
Codon Usage Db - The frequency of codon use in each organism is made searchable through this World Wide Web site.
EPD - Eukaryotic Promoter db
HOVERGEN - Homologous Vertebrate Genes db
IMGT - ImMunoGeneTics db [Mirror at EBI]
ISIS - Intron Sequence and Information System
RDP - Ribosomal db Project
gRNAs db - Guide RNA db
PLACE - Plant cis-acting regulatory DNA elements db
PlantCARE - Plant cis-acting regulatory DNA elements db
sRNA db - Small RNA db
ssu rRNA - Small ribosomal subunit db
lsu rRNA - Large ribosomal subunit db
5S rRNA - 5S ribosomal RNA db
tmRNA Website
tmRDB - tmRNA dB
tRNA - tRNA compilation from the University of Bayreuth
uRNADB - uRNA db
RNA editing - RNA editing site
RNAmod db - RNA modification db
TelDB - Multimedia Telomere Resource
TRADAT - TRAnscription Databases and Analysis Tools
Subviral RNA db - Small circular RNAs db (viroid and viroid-like) MPDB - Molecular probe db
OPD - Oligonucleotide probe db
VectorDB - Vector sequence db

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二　基因表达数据库

ASDB - Protein products and expression patterns of alternatively-spliced genes
Axeldb - Gene expression in Xenopus
BodyMap - Human and mouse gene expression data
EpoDB - Genes expressed in vertebrate RBC
FlyView - Drosophila development and genetics
Gene Expression Database (GXD) - Mouse gene expression and genomics
Kidney Development Database - Kidney development and gene expression
MAGEST - Ascidian (Halocynthia roretzi) gene expression patterns
Mouse Atlas and Gene Expression Database - Spatially-mapped gene expression data
PEDB - Normal and aberrant prostate gene expression
Tooth Development Database - Gene expression in dental tissue
TRIPLES - TRansposon-Insertion Phenotypes, Localization and Expression in Saccharomyces

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三。　蛋白质及其相关数据库

1.蛋白质序列和相关数据库

SWISS-PROT - SWISS-PROT annotated protein sequence db
PIR-international -The Protein Information Resource (protein sequence)
MIPS - Martinsried institute for protein sequence and homology data and yeast genome information
PROSITE - PROSITE dictionary of protein sites and patterns
InterPro - Integrated Resources of Proteins Domains and Functional Sites
BLOCKS - BLOCKS db
DOMO - Protein domain db (Automatically generated)
Pfam - Protein families db (HMM derived) [Mirror at Sanger]
PRINTS - Protein Motif fingerprint db
ProDom - Protein domain db (Automatically generated)
PROTOMAP - An automatic hierarchical classification of SWISS-PROT proteins
SBASE - SBASE domain db (Protein domain sequence library)
SMART - Protein signalling and extracellular domain patterns (Simple Modular Architecture Research Tool)
ProClass - Protein sequence alignments and curation of protein families
Kabat - Kabat db of protein of immunological interest
PMD - Protein Mutant db 　
2.蛋白质三维结构和相关数据库

PDB - Protein Data Bank [Mirrors in EBI]
BioMagResBank - Repository for data on proteins, peptides, and nucleic acids from NMR spectroscopy
SWISS-MODEL Repository - Automatically generated protein models db
ModBase - Db of comparative protein structure models
CATH - UCL BSM structural classification of proteins
SCOP - Structural classification of proteins [Mirror at USA | Israel | Singapore | Australia]
Mol_R_Us - Molecules R Us, browser for PDB
BMM Domain Server - Biomolecular Modelling Laboratory (ICRF) protein domain server
PRESAGE - Collaborative resource for structural genomics
ReLiBase - Receptor/ligand complexes db [Mirror in USA]
TOPS - Protein topology atlas
CCDC - Cambridge Crystallographic Data Center (Cambridge Stuctural Db (CSD))　
HSSP - Homology-derived secondary structure of proteins db
SWISS-3DIMAGE - 3D images of proteins and other biological macromolecules
BioImage - Biological image db (contains imaging data on macromolecules) 　
3.蛋白质二维凝胶电泳数据库

WORLD-2DPAGE - A complete index of 2D-PAGE db and servers
Phoretix links - Phoretix page of links to 2D gel db
4.信号传导及蛋白质-蛋白质相互作用相关数据库

DIP - Db of Interacting Proteins
INTERACT - Protein-Protein interaction db
ProNet - Protein-Protein interaction db　
CANSITE - Signal Transduction's Web
SPAD - Signaling pathway db
CSNDB - Cell Signaling Networks db 　
5.DNA和蛋白质相互作用数据库

DPInteract - DNA-Proteins interactions db

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　 四。特定基因或蛋白质的数据库
AAA - AAA family of ATPases server
Acetylcholinesterases
ALDH - Aldehyde dehydrogenase gene superfamily db
Aminoacyl-tRNA synthetases in SWISS-PROT - List of aminoacyl-tRNA synthetases in SWISS-PROT
AARSDB - Aminoacyl-tRNA synthetases db
Allergens in SWISS-PROT - Nomenclature and index of allergens in SWISS-PROT
AMSDb - Antimicrobial sequences db
Antibody resource page - Links to antibody related Web resources
Australian venom and toxin db
Bacillus thuringiensis toxin specificity db
TFII - Basal transcription factors
Blood group antigens in SWISS-PROT
BCGD - Breast cancer genes db from MBCR
BRENDA - Db of enzyme functional data
EF-hand CaBP - EF-hand calcium-binding proteins db
CAZy - Carbohydrate-Active enZYmes Web site
CBS domain - Cystathionine Beta Synthase domain WWW page
CD antigens in SWISS-PROT - Nomenclature for surface proteins of human leucocytes (CD)
CD antigens in PROW - Database on information about CD antigens
Chaperonin - Information on GroEL and GroES chaperonins
Conotoxins - Information on conotoxins from a Web site on cone shells
Cytokines Web - Structure and function of cytokines and their receptors
COPE - Cytokines On-line Pathfinder Encyclopedia [Mirror in Israel]
dbCFC - Cytokine family cDNA db
R&D Systems' Cytokine Source Book
DExH/D protein family db
ENZYME - Enzymes nomenclature db
Worthington enzyme manual
Eph - Eph receptor tyrosine kinases and their ligands (ephrins) resource
EpoDB - Erythropoiesis gene expression db (Epo GED)
ESTHER - Esterases and alpha/beta hydrolase enzymes
Expansins web site
Modules - Extracellular proteins modules (domains)
FADPNR - FAD-dependent pyridine nucleotide oxidoreductases
Flavodoxins
FlyNets - Db of molecular interactions in Drosophila melanogaster
FYVE finger domain
GABAagent - GABA receptors WWW site
Globin - Globin gene server
Glucoamylases
Glycosyl hydrolases in SWISS-PROT - Nomenclature and index of glycosyl hydrolases in SWISS-PROT
7TM in SWISS-PROT - List of G protein coupled receptors in SWISS-PROT
GCRDb - G protein-coupled receptor db
GPCRDB - G protein-coupled receptor db (7TM) at EMBL
ORDB - Olfactory receptor db
GRAP - G protein coupled receptors family A mutants db
GRR - Glucocorticoid receptor resource
Glycosyltransferases - A guide to cloned glycosyltransferases
GnRH - Gonadotropin-releasing hormones (GnRH) family
GyrB - GyrB protein
Yeast RNA helicases
Histone - Histones db
HIVdb - HIV protease db
HotMolecBase - Molecules (mainly proteins) that are promising targets for medical applications
Homeobox - Homeobox domain proteins resource
HOX-Pro - Homeobox genes db
Hox proteins in SWISS-PROT - Vertebrate homeotic Hox proteins: nomenclature and index of SWISS-PROT entries
Labial - Homeobox genes, labial family
HSP100 - HSP100/ClpAB family of chaperones
InBase - Inteins db from the New England Biolabs
Integrins
ICN - The Ion Channel Network
KEGG - Kyoto Encyclopedia of Genes and Genomes
Kinesin - Kinesin motor proteins
Klotho - Biochemical compounds declarative db
LGIC - Ligand Gated Ion Channel subunit db
LED - Lipase Engineering Database
MDB - Metalloprotein Site Database and Browser
Metallothioneins in SWISS-PROT - Nomenclature and index of metallothioneins in SWISS-PROT
MT - Metallothioneins
MHCPEP - MHC binding peptides db
SYFPEITHI - MHC ligands and peptide motifs db
Mitochondrial carriers pages from Nelson's lab
MitoPick - Mitochondrial NADH-ubiquinone reductase (complex I) web site
MRR - Mineralocorticoid receptor resource
Mutator - Transposases, Mutator family
MutBase - Mutation spectra db (Db on mutants of several bacterial and mammalian genes)
MutS - MutS family
Neurotrophic factors
NucleaRDB - Federated db on nuclear receptors
P450 pages from Nelson's lab
P450 - Directory of P450-containing systems
IARC p53 db - IARC db of somatic p53 mutations
PDZ domain - PDH/DHR domain WWW page
PDE - Phosphodiesterases
Peroxidases
Plant Peroxidases
Peptidases in SWISS-PROT - Nomenclature and index of peptidases in SWISS-PROT
MEROPS - Peptidase db
Prolysis - Proteases and inhibitors server
Protein Degradation Resource
PLACE - Plant cis-acting regulatory DNA elements db
PlantCARE - Plant cis-acting regulatory DNA elements db
PKR - Protein Kinase Resource
PatBase - P-type ATPase db
PPAR - Peroxisome Proliferator-Activated Receptor resource
PPDB - Phosphoprotein db
Proteoglycans
Phytochromes - Computer analysis of phytochrome sequences
RecA - RecA protein
REBASE - Restriction enzymes and methylases db
Restriction enzymes/methylases in SWISS-PROT - List of restriction enzymes and methylases in SWISS-PROT
Ribosomal proteins in SWISS-PROT - Families and index of ribosomal proteins in SWISS-PROT
Ribosomal proteins - Analysis of R proteins by Nikos Kyrpides
RNase P - Ribonuclease P db
SRPDB - Signal Recognition Particle db
SNF2 - SNF2 family
TRR - Thyroid hormone receptors resource
Topoisomerases - Type I and II topoisomerases
TRANSFAC - Transcription factors db
TRANSPATH - Signal Transduction Browser
Transport Classification System - from Milton Saier
UDP Glucuronosyltransferases
V BASE - Directory of human V gene sequences (Immunoglobulin germline variable region)
VDRR - Vitamin D receptor resource
WD-repeat - WD-repeat proteins family
WIT - 'What is There' metabolic models db
WormPep - C.elegans proteins db
YTPdb - Yeast Transport Protein db

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五 糖类相关数据库

CarbBank - Complex Carbohydrate Structure Database
GlycoSuiteDB - Db of glycan structures
TGN - The Glycoscience Network
FCCA - Forum Carbohydrates Coming of Age
CARBHYD - Carbohydrate information WWW sites
Monosacharide browser - Space filling Fischer projection for monosaccharides

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六 蛋白质翻译后修饰相关数据库

O-GlycBase - O-glycosylated proteins db
PhosphoBase - Phosphorylation sites db
RESID - Db of Amino Acid Modifications

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七 人类基因突变及疾病相关数据库

HMGD - Human Gene Mutation db
SVD - Sequence variation db
HGBASE - Human Genic Bi-Allelic Sequences db
The SNP consortium
dbSNP - Human single nucleotide polymorphism (SNP) db 　
List of mutation databases from OMIM
List of mutation databases from IMT (Finland) 　
ADB - Albinism db (Mutations in human genes causing albinism)
Alpha-glucosidase - Information about human acid alpha-glucosidase (GSD-II)
AR mutations - Human androgen receptor mutation db
Antithrombin mutation db
Asthma and Allergy gene db
BIOMDB - Db of mutations causing tetrahydrobiopterin deficiencies
BLMbase - Human BLM mutation db (Bloom snydrom)
BTKbase - Human BTK mutation db (X-linked agammaglobulinemia)
CD40Lbase - Human CD40 ligand mutation db
COL1/3 mutation - Human Type I and III collagen mutation db
CFTR mutation - Human cystic fibrosis mutation db (CFTR)
EMD db - Human Emerin (EMD) mutation db (Emery-Dreifuss muscular dystrophy)
KMeyeDB - Eye disease genes db
FVII mutation - Human Factor VII mutation db
HAMSTeRS - Human Factor VIII mutation db (Haemophilia A)
HAeMB - Human Factor IX mutation db (Haemophilia B)
FBN1 mutation - Human fibrillin 1 mutation db (Marfan syndrome)
G6PD - Human G6PD deficiency resource
Galt mutation - Human galactose-1-phosphate uridylyltransferase mutation db (Galactosemia)
HEXAdb - Human Hexosaminidase A mutation db (Tay-sachs disease)
IL2RGbase - Human IL2RG (Interleukin-2 receptor gamma) mutation db (X-SCID)
L1CAM mutation - Human L1CAM mutation db
LDLR mutation - Human LDLR mutation db (Familial hypercholesterolemia)
LQTSdb - Long QT syndrome db
NCF1base - Human NCF1 mutation db
NCF2base - Human NCF2 mutation db
Neuromuscular diseases web site
NCL - Neuronal Ceroid Lipofuscinoses mutation db
OTCase - Human ornithine transcarbamylase (OTCase) website
Cytochrome P450 alleles nomenclature
p53 mutation db - University of Tokyo p53 mutation db
Germline p53 mutation db - University of Prague db of germline p53 mutations
PAHdb - Human phenylalanine hydroxylase (PAH) mutation db
PAX6 mutation - Human PAX6 mutation db
Prion - Prion and prion disease web site
RAG1base - Human RAG1 mutation db
RAG2base - Human RAG2 mutation db
RB1base - Human retinoblastoma-associated protein (RB) mutation db
RetNet - Retinal Information Network
Retina International Scientific Newsletter - Information on Retinal genes, proteins and diseases
TSC - TSC (TSC1/TSC2) variation db
TSC2 - Cardiff-Rotterdam Tuberous Sclerosis (TS) db (Tuberin; TSC2)
TGDB - Tumor gene db
VMD2 mutation - Human VMD2 mutation db
vWF mutation - Human von Willebrand factor (vWF) mutation db
WRN - Human WRN mutation db (Warner disease)
WT1 mutation - Human WT1 mutation db
X-ALD mutation - Human ABCD1 mutation db

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八 进化相关数据库及资源

Clusters of Orthologous Groups (COG) - Phylogenetic classification of proteins from 21 complete genomes
XREFdb - Cross-referencing of model organism genetics with mammalian phenotypes
TreeBASE - Relational db of phylogenetic information
The Tree of life - Collection of WWW pages on phylogeny and biodiversity of organisms

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九 专利数据库

DPD - DNA Patent db
Ag Patents - Agricultural Biotechnology patents from the USDA 　
USPTO patent db - USA Patent and Trademark Office patent db
Esp@cenet - Patent information database from the European Patent Office (worldwide coverage)
The Delphion Intellectual Property Network (IPN) for searching, viewing, and analyzing patent documents.