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生物信息分析常用数据库:2012年终结者篇(二)  

2012-06-07 09:16:31|  分类: 生物信息分析 |  标签: |举报 |字号 订阅

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4. Structure Databases
4.1. Small molecules



Database name
Full name and/or description
URL
ChEBI
Chemical entities of biological interest
CSD
Cambridge structural database: crystal structure information for organic and metal-organic compounds
HIC-Up
Hetero-compound Information Centre? Uppsala
AANT
Amino acid?nucleotide interaction database
Klotho
Collection and categorization of biological compounds
LIGAND
Chemical compounds and reactions in biological pathways
PDB-Ligand
3D structures of small molecules bound to proteins and nucleic acids
Ligand Depot
Ligand Depot is a data warehouse which integrates databases, services, tools and methods related to small molecules bound to macromolecules.
PubChem
Structures and biological activities of small organic molecules
4.2. Carbohydrates



Database name
Full name and/or description
URL
CCSD
Complex carbohydrate structure database (CarbBank)
CSS
Carbohydrate structure suite: carbohydrate 3D structures derived from the PDB
Glycan
Carbohydrate database, part of the KEGG system
GlycoSuiteDB
N- and O-linked glycan structures and biological sources
Monosaccharide Browser
Space-filling Fischer projections of monosaccharides
SWEET-DB
Annotated carbohydrate structure and substance information
4.3. Nucleic acid structure



Database name
Full name and/or description
URL
NDB
Nucleic acid-containing structures
NTDB
Thermodynamic data for nucleic acids
RNABase
RNA-containing structures from PDB and NDB
SCOR
Structural classification of RNA: RNA motifs by structure, function and tertiary interactions
4.4. Protein structure



Database name
Full name and/or description
URL
ArchDB
Automated classification of protein loop structures
wwPDB
Worldwide Protein Data Bank
PDBj
Protein Data Bank Japan-the archive for macromolecular structures.
ASTRAL
Sequences of domains of known structure, selected subsets and sequence? structure correspondences
BAliBASE
A database for comparison of multiple sequence alignments
BioMagResBank
NMR spectroscopic data for proteins and nucleic acids
CADB
Conformational angles in proteins database
CATH
Protein domain structures database
CE 3D
protein structure alignments
CKAAPs DB
Structurally similar proteins with dissimilar sequences
Dali
Protein fold classification using the Dali search engine
Decoys ?R' Us
Computer-generated protein conformations
DisProt
Database of Protein Disorder: proteins that lack fixed 3D structure in their native states
DomIns
Domain insertions in known protein structures
DSDBASE
Native and modeled disulfide bonds in proteins
DSMM
Database of simulated molecular motions
eF-site
Electrostatic surface of Functional site: electrostatic potentials and hydrophobic properties of the active sites
GenDiS
Genomic distribution of protein structural superfamilies
Gene3D
Precalculated structural assignments for whole genomes
GTD
Genomic threading database: structural annotations of complete proteomes
GTOP
Protein fold predictions from genome sequences
Het-PDB
Navi Hetero-atoms in protein structures
HOMSTRAD
Homologous structure alignment database: curated structure-based alignments for protein families
IMB Jena Image Library
Visualization and analysis of 3D biopolymer structures
IMGT/3Dstructure-DB
Sequences and 3D structures of vertebrate immunoglobulins, T cell receptors and MHC proteins
ISSD
Integrated sequence?structure database
LPFC
Library of protein family core structures
MMDB
NCBI's database of 3D structures, part of NCBI Entrez
E-MSD
EBI's macromolecular structure database
ModBase
Annotated comparative protein structure models
MolMovDB
Database of macromolecular movements: descriptions of protein and macromolecular motions, including movies
PALI
Phylogeny and alignment of homologous protein structures
PASS2
Structural motifs of protein superfamilies
PepConfDB
A database of peptide conformations
PDB
Protein structure databank: all publicly available 3D structures of proteins and nucleic acids
PDB-REPRDB
Representative protein chains, based on PDB entries
PDBsum
Summaries and analyses of PDB structures
PDB_TM
Transmembrane proteins with known 3D structure
Protein Folding Database
Experimental data on protein folding
SCOP
Structural classification of proteins
Sloop
Classification of protein loops
Structure Superposition Database
Pairwise superposition of TIM-barrel structures
SWISS-MODEL Repository
Database of annotated 3D protein structure models
SUPERFAMILY
Assignments of proteins to structural superfamilies
SURFACE
Surface residues and functions annotated, compared and evaluated: a database of protein surface patches
TargetDB
Target data from worldwide structural genomics projects
3D-GENOMICS
Structural annotations for complete proteomes
TOPS
Topology of protein structures database
5. Genomics Databases (non-human)
5.1. Genome annotation terms, ontologies and nomenclature



Database name
Full name and/or description
URL
Genew
Human gene nomenclature: approved gene symbols
GO
Gene ontology consortium database
GOA
EBI's gene ontology annotation project
IUBMB Nomenclature database
Nomenclature of enzymes, membrane transporters, electron transport proteins and other proteins
IUPAC Nomenclature database
Nomenclature of biochemical and organic compounds approved by the IUBMB-IUPAC Joint Commission
IUPHAR-RD
The International Union of Pharmacology recommendations on receptor nomenclature and drug classification
PANTHER
Gene products organized by biological function
UMLS
Unified medical language system
5.1.1. Taxonomy and Identification



Database name
Full name and/or description
URL
ICB
gyrB database for identification and classification of bacteria
NCBI Taxonomy
Names of all organisms represented in GenBank
PANDIT
Protein and associated nucleotide domains with inferred trees
RIDOM
rRNA-based differentiation of medical microorganisms
RDP-II
Ribosomal database project
Tree of Life
Information on phylogeny and biodiversity
5.2. General genomics databases



Database name
Full name and/or description
URL
COG
Clusters of orthologous groups of proteins
COGENT
Complete genome tracking: predicted peptides from fully sequenced genomes
CORG
Comparative regulatory genomics: conserved non-coding sequence blocks
DEG
Database of essential genes from bacteria and yeast
EBI Genomes
EBI's collection of databases for the analysis of complete and unfinished viral , pro- and eukaryotic genomes
EGO
Eukaryotic gene orthologs: orthologous DNA sequences in the TIGR gene indices
EMGlib
Enhanced microbial genomes library: completely sequenced genomes of unicellular organisms
Entrez Genomes
NCBI's collection of databases for the analysis of complete and unfinished viral , pro- and eukaryotic genomes
ERGO
Light Integrated biochemical data on nine bacterial genomes: publicly available portion of the ERGO database
FusionDB
Database of bacterial and archaeal gene fusion events
Genome Atlas
DNA structural properties of sequenced genomes
Genome Information Broker
DDBJ's collection of databases for the analysis of complete and unfinished viral , pro- and eukaryotic genomes
Genome Reviews
Integrated view of complete genomes
GOLD
Genomes online database: a listing of completed and ongoing genome projects
HGT-DB
Putative horizontally transferred genes in prokaryotic genomes
Integr8
Functional classification of proteins in whole genomes
KEGG
Kyoto encyclopedia of genes and genomes: integrated suite of databases on genes , proteins and metabolic pathways
MBGD
Microbial genome database for comparative analysis
ORFanage
Database of orphan ORFs (ORFs with no homologs) in complete microbial genomes
PACRAT
Archaeal and bacterial intergenic sequence features
PartiGeneDB
Assembled partial genomes for _ 250 eukaryotic organisms
PEDANT
Results of an automated analysis of genomic sequences
TIGR Microbial Database
Lists of completed and ongoing genome projects with links to complete genome sequences
TIGR Comprehensive Microbial Resource
Various data on complete microbial genomes: uniform annotation, properties of DNA and predicted proteins
TransportDB
Predicted membrane transporters in complete genomes, classified according to the TC classification system
WIT3
What is there ? Metabolic reconstruction for completely sequenced microbial genomes

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