Interesting links for Structural Genomics
Proteins
NR All non-redundant GenBank CDS translations+PDB+SwissProt+PIR
OWL A non-redundant composite of 4 publicly-available primary sources: SWISS-PROT, PIR (1-3), GenBank (translation) and NRL-3D.
SWISSPROT A curated protein sequence database
trEMBL A supplement of SWISS-PROT that contains all the translations of EMBL nucleotide sequence entries not yet integrated in SWISS-PROT
PIR A comprehensive, annotated, and non-redundant set of protein sequence databases in which entries are classified into family groups and alignments of each group are available.
PDB An archive of experimentally determined three-dimensional structures of biological macromolecules
UNIGENE An experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters.
dbEST A division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or Expressed Sequence Tags, from a number of organisms.
Families
PIR/MIPS Classification by protein (super)family and homology domains
Proclass A non-redundant protein database organized according to family relationships as defined collectively by ProSite patterns and PIR superfamilies.
prodom Protein domain database consists of an automatic compilation of homologous domains. from SWISS-PROT 36 + TREMBL +TREMBL updates
DOMO Protein domain database consists of an automatic compilation of domains from SwissProt and PIR
SBASE A protein cluster database
protomap An classification of all proteins in the swissprot database, into clusters of related proteins.
pfam A large collection of multiple sequence alignments and hidden Markov models covering many common protein domains.
Picasso PSSP (Protein Sequence Space Partitioning) is derived from nrdb90 (from Mar'98).
SYSTERS The clustering of the PIR1 (Rel. 51) and the SWISS-PROT (Rel.34) databases
Molecular Sequence Megaclassification A server provides access to a non-redundant molecular sequence collection that has been classified by different research groups.
BLOCKS Multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins.
PROSITE A database of protein families and domains. It consists of biologically significant sites, patterns and profiles that help to reliably identify to which known protein family (if any) a new sequence belongs
prints A compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of OWL.
HSSP A database of homology-derived secondary structure of proteins.
COG Clusters of Orthologous Groups (COGs) were delineated by comparing protein sequences encoded in 8 complete genomes, representing 6 major phylogenetic lineages.
Structure Classfication
Dali/FSSP A network service for comparing protein structures in 3D.
SCOP Structural Classification of Proteins.
CATH A novel hierarchical classification of protein domain structures, which clusters proteins at four major levels, class(C), architecture(A), topology(T) and homologous superfamily (H).
Genome
SGD A scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae
YPD A protein database with emphasis on the physical and functional properties of the yeast proteins.
MIPS The Yeast Genome database
Yeast Gene Duplications This Web site contains data on duplicated genes in the yeast (Saccharomyces cerevisiae) genome.
atDB Arabidopsis thaliana Genome Database
Haemophilus influenzae Genome information for Haemophilus influenzae
FlyBase A Database of the Drosophila Genome
ACEDB A Database of the C. elegans Genome
MDG Mouse Genome Informatics
TIGR Microbial Database A listing of microbial genomes and chromosomes completed and in progress
Human
GDB The official central repository for genomic mapping data resulting from the Human Genome Initiative.
HGMD Human Gene Mutation Database
OMIM Online Mendelian Inheritance in Man. A catalog of human genes and genetic disorders
CGAP An interdisciplinary program to establish the information and technological tools needed to decipher the molecular anatomy of a cancer cell.
GeneCard A database of human genes, their products and their involvement in diseases.
HUGO Human Gene Nomenclature Committee
TGDB The Tumor Gene Database
Functions
WIT An environment for interpreting sequenced genomes for supporting metabolic reconstruction .
KEGG Kyoto Encyclopedia of Genes and Genomes
DIP Database of Interacting Proteins
Yeast Expression Database This website contains the complete data sets for the experiments in the paper - DeRisi et. al. Science 278: 680-686, as well as the images of the whole-genome microarrays.
signaling  
HIC-Up A reesource for structural biologists dealing with hetero-compounds
ReliBase A database system for analysing receptor/ligand complexes deposited in the Brookhaven Protein Databank.
Prediction
TMpred A program makes a prediction of membrane-spanning regions and their orientation.
TMAP Transmembrane protein fragment prediction program
DAS Transmembrane protein fragment prediction program
SOUSI Transmembrane protein fragment prediction program
COILS Coiled coil fragment prediction program
Paircoil Coiled coil fragment prediction program
The PredictProtein server PHDsec, PHDacc, PHDhtm, PHDtopology, TOPITS, MaxHom, EvalSec
PREDATOR A secondary structure prediction
GOR IV A secondary structure prediction
NNPREDICT A secondary structure prediction
SSPRED A secondary structure prediction
123D A threading program to use residue-residue contact potentials for checking the compatibility of 3D structures with a sequence (1D).
UCLA-DOE A threading protein structure prediction sever. Besides threading, it also interages some other sequence and structure prediction and analysis software around the world.
Threader A threading protein structure prediction program
Swiss-Model An Automated Comparative Protein Modelling Server
MODELLER A program for homology protein structure modelling by satisfaction of spatial restraints.
Calculations
Peptide Mass Compute peptide Mass
Compute pI/Mw tool Compute pI/Mw tool
Translate tool a tool which allows the translation of a nucleotide (DNA/RNA) sequence to a protein sequence.
CLUSTALW A Multiple sequence align program
MSA A Multiple sequence align program
Multalin A Multiple sequence align program
ALIGN A Multiple sequence align program
AMAS A Multiple sequence align program
NCBI BLAST programs NCBI's sequence similarity search tool designed to support analysis of nucleotide and protein databases.
GCG Software for the Analysis of Genes and Proteins
GeneQuiz A system provides automated analysis of biological sequences.
Others
PRESAGE A database of proteins for structural genomics, it has both experimental and theorical predition information.
PSI Protein Structure Initiative Database. A database help selecting and tracking protein targets
PubMed A literature reference database
ENZYME A repository of information relative to the nomenclature of enzymes.
TUTORIAL Terry Gaasterland's TUTORIAL ON The Role of Computational Biology In High-Throughput Structure Determination