[转载]结构数据库

4. Structure Databases
4.1. Small molecules
AANT	Amino Acid - Nucleotide interaction database	http://aant.icmb.utexas.edu/
ChEBI	Chemical entities of biological interest	http://www.ebi.ac.uk/chebi/
ChemBank	Structures and biological activities of small organic molecules	http://chembank.broad.harvard.edu/
ChemDB	3D structures and properties of small molecules	http://cdb.ics.uci.edu
CSD	Cambridge Structural Database	http://www.ccdc.cam.ac.uk/prods/csd/csd.html
Het-PDB Navi	Hetero-atoms in protein structures	http://daisy.bio.nagoya-u.ac.jp/golab/hetpdbnavi.html
HIC-Up	Hetero-compound Information Centre - Uppsala	http://xray.bmc.uu.se/hicup/
Klotho	Collection and categorization of biological compounds	http://www.biocheminfo.org/klotho/
LIGAND	Chemical compounds and reactions in biological pathways	http://www.genome.ad.jp/ligand/
PDB-Ligand	3D structures of small molecules bound to proteins and nucleic acids	http://www.idrtech.com/PDB-Ligand/
PubChem	Structures and biological activities of small organic molecules	http://pubchem.ncbi.nlm.nih.gov/
R.E.DD.B.	RESP and ESP atomic charges and force field libraries for small molecules and molecular fragments	http://q4md-forcefieldtools.org/REDDB
4.2. Carbohydrates
BCSDB/Glycoscience	Bacterial Carbohydrate Structure DataBase	http://www.glyco.ac.ru/bcsdb/start.shtml
CarbBank	CCSD - Complex Carbohydrate Structure Database	http://bssv01.lancs.ac.uk/gig/pages/gag/carbbank.htm
CSS	Carbohydrate Structure Suite: carbohydrate 3D structures	http://www.dkfz.de/spec/css/
Glycan	Carbohydrate database, part of the KEGG system	http://glycan.genome.ad.jp/
Glycoconjugate Data Bank	Annotated structures of glycan molecules	http://daisy2.nagahama-i-bio.ac.jp/structures/
GlycoMaps DB	Conformational maps of disaccharides	http://www.glycosciences.de/modeling/glycomapsdb/
GlycoSuiteDB	N- and O-linked glycan structures and biological sources	http://www.glycosuite.com
Monosaccharide Browser	Space filling Fischer projections of monosaccharides	http://www.terravivida.com/vivida/monosaccharide/
SWEET-DB	Annotated carbohydrate structure and substance information	http://www.dkfz-heidelberg.de/spec2/sweetdb/
4.3. Nucleic acid structure
Greglist	G-quadruplex motifs and potentially G-quadruplex regulated genes	http://tubic.tju.edu.cn/greglist/
ITS2	Predicted structures of internal transcribed spacer 2 (ITS2) molecules	http://its2.bioapps.biozentrum.uni-wuerzburg.de/ITS2_db.html
NDB	Nucleic acid-containing structures	http://ndbserver.rutgers.edu/
NTDB	Thermodynamic data for nucleic acids	http://ntdb.chem.cuhk.edu.hk
QuadBase	G-quadruplex motifs in the promoters of human, chimpanzee, rat, mouse and bacterial genes	http://quadbase.igib.res.in/
RNA FRABASE	Database of 3D RNA fragments within known RNA structures	http://rnafrabase.ibch.poznan.pl/
RNABase	RNA-containing structures from PDB and NDB	http://www.rnabase.org
RNAJunction	RNA structural elements: helical junctions, internal loops, bulges and loop-loop interactions	http://rnajunction.abcc.ncifcrf.gov
SARS-CoV RNA SSS	Predicted secondary structures of SARS coronavirus RNA	http://www.liuweibo.com/sarsdb/
SCOR	Structural classification of RNA: RNA motifs by structure, function and tertiary interactions	http://scor.lbl.gov
4.4. Protein structure
3D-Genomics	Structural annotations for complete proteomes	http://www.sbg.bio.ic.ac.uk/3dgenomics
3DID	3D interacting domains	http://gatealoy.pcb.ub.es/3did/
ArchDB	Automated classification of protein loop structures	http://gurion.imim.es/archdb
ASTRAL	Sequences of domains of known structure, selected subsets and sequence-structure correspondences	http://astral.berkeley.edu/
AutoPSI	Automated structural classification of protein sequences	http://www.bio.ifi.lmu.de/AutoPSIDB
BioMagResBank	NMR spectroscopic data from proteins, peptides, and nucleic acids	http://www.bmrb.wisc.edu/
CADB	Conformational Angles DataBase of Proteins	http://cluster.physics.iisc.ernet.in/cadb/
CATH	Protein domain structures database	http://www.cathdb.info/
CE	Combinatorial Extension method to compute and review 3D protein structure alignments	http://cl.sdsc.edu/ce.html
CKAAPs DB	Conserved Key Amino Acid Positions Database	No longer maintained
CoC Central	Universally conserved residues in protein folds	http://kulibin.mit.edu/coc/
ColiSNP	Mapping non-synonymous SNPs on protein structures	http://yayoi.kansai.jaea.go.jp/colisnp
Columba	Annotation of protein structures from the PDB	http://www.columba-db.de
Dali database	Fold classification based on structural alignment of proteins	http://ekhidna.biocenter.helsinki.fi/dali/start
DBAli	Database of structure alignments	http://salilab.org/DBAli/
Decoys-R-Us	Computer-generated protein conformations based on sequence data	http://dd.compbio.washington.edu/
DisProt	Database of Protein Disorder	http://divac.ist.temple.edu/disprot
DMAPS	Database of multiple alignments for protein structures	http://bioinformatics.albany.edu/~dmaps
DSDBASE	Disulfide Database	http://www.ncbs.res.in/~faculty/mini/dsdbase/dsdbase.html
DSMM	A Database of Simulated Molecular Motions	http://projects.villa-bosch.de/dbase/dsmm/
E-MSD	EBI-Macromolecular Structure Database	http://www.ebi.ac.uk/msd
FSN	Flexible structural neighborhood, structural neighbors of proteins identified by FATCAT tool	http://fatcat.ljcrf.edu/fatcat-cgi/cgi/struct_neibor/fatcatStructNeibor.pl
FSSP		Superseded by the Dali database, no. 442
Gene3D	Precalculated structural assignments for whole genomes	http://cathwww.biochem.ucl.ac.uk:8080/Gene3D/
Genomic Threading DB	Structural annotations of complete genomes	http://bioinf.cs.ucl.ac.uk/GTD
GTOP	Protein fold predictions from genome sequences	http://spock.genes.nig.ac.jp/~genome/gtop.html
HOMSTRAD	Homologous structure alignment database: curated structure-based alignments for protein families	http://www-cryst.bioc.cam.ac.uk/homstrad
IMB Jena Image Library	Visualization and analysis of 3D biopolymer structures	http://www.imb-jena.de/IMAGE.html
IMGT/3Dstructure-DB	3D structures of Immunoglobulins, T cell receptors, and MHC proteins	http://imgt3d.igh.cnrs.fr/
IMOTdb	Spatially interacting motifs in proteins	http://caps.ncbs.res.in/imotdb/
LPFC	Library of protein family core structures	http://helix-web.stanford.edu/LPFC/
MMDB	All experimentally-determined 3D structures, linked to NCBI Entrez	http://www.ncbi.nlm.nih.gov/Structure/
ModBase	Annotated comparative protein structure models	http://salilab.org/modbase
MolMovDB	Database of Macromolecular Movements	http://bioinfo.mbb.yale.edu/MolMovDB/
MPID	MHC-Peptide Interaction Database	http://surya.bic.nus.edu.sg/mpidt
PASS2	Structural motifs of protein superfamilies	http://www.ncbs.res.in/~faculty/mini/campass/pass2.html
PDB	Protein Data Bank: all known protein structures	http://www.pdb.org/
PDB_TM	Transmembrane proteins with known 3D structure	http://pdbtm.enzim.hu/
PDB-REPRDB	Representative protein chains, based on PDB entries	http://mbs.cbrc.jp/pdbreprdb-cgi/reprdb_menu.pl
PDBsum	Summaries and analyses of PDB structures	http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/
PepConfDB	Database of peptide conformations	http://www.peptidome.org/products/list.htm
PFD	Protein Folding Database : Experimental data on protein folding	http://www.foldeomics.org/pfd/public_html/index.php
PMDB	3D protein models obtained from structure predictions	http://www.caspur.it/PMDB/
RESID	Post-translational modifications of proteins	http://www.ebi.ac.uk/RESID/
S4	Structure-based Sequence Alignments of SCOP Superfamilies	http://compbio.mds.qmw.ac.uk/~james/S4.shtml
SCOP	Structural classification of proteins	http://scop.mrc-lmb.cam.ac.uk/scop
SCOPPI	Structural classification of protein-protein interfaces	http://www.scoppi.org
SLoop	Classification of protein loops	http://www-cryst.bioc.cam.ac.uk/~sloop/
SSToSS	Sequence-Structural Templates of Single-member Superfamilies	http://caps.ncbs.res.in/SSTOSS/index.htm
STING Report	Amino acid properties in proteins of known structure	http://sms.cbi.cnptia.embrapa.br/SMS/STINGm/SMSReport/
Structure Superposition Database	Pairwise superpositions of 115 TIM-barrel structures	http://ssd.rbvi.ucsf.edu/
SUPERFAMILY	Assignments of proteins to structural superfamilies	http://supfam.org/SUPERFAMILY/
SURFACE	Surface residues and functions annotated, compared and evaluated: a database of protein surface patches	http://cbm.bio.uniroma2.it/surface
SWISS-MODEL Repository	3D protein structure models generated by automated homology modeling using SWISS-MODEL	http://swissmodel.expasy.org/repository
TargetDB	Target data from worldwide structural genomics projects	http://targetdb.pdb.org/
TMBETA-GENOME	Beta-barrel membrane proteins encoded in various genomes	http://tmbeta-genome.cbrc.jp/annotation/
TOPOFIT-DB	Protein structural alignments based on the TOPOFIT method	http://mozart.bio.neu.edu/topofit/
TOPS	Topology Of Protein Structures	http://www.tops.leeds.ac.uk

 

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