Interesting links for Structural Genomics
| Proteins |
| NR
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All non-redundant GenBank CDS translations+PDB+SwissProt+PIR
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| OWL |
A non-redundant composite of 4 publicly-available primary sources: SWISS-PROT,
PIR (1-3), GenBank (translation) and NRL-3D.
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| 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
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| 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.
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| PDB |
An archive of experimentally determined
three-dimensional structures of biological macromolecules
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| UNIGENE |
An experimental system for automatically partitioning
GenBank sequences into a non-redundant set of gene-oriented
clusters.
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| 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.
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| 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.
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| prodom |
Protein domain database consists of an automatic compilation of homologous
domains. from SWISS-PROT 36 + TREMBL +TREMBL updates
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| DOMO |
Protein domain database consists of an automatic compilation of domains
from SwissProt and PIR
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| SBASE |
A protein cluster database
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| protomap |
An classification of all proteins in the
swissprot database, into clusters of related proteins.
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| pfam |
A large collection of multiple sequence alignments and hidden Markov models
covering many common protein domains.
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| Picasso |
PSSP (Protein Sequence Space Partitioning) is derived from nrdb90 (from
Mar'98).
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| SYSTERS |
The clustering of the PIR1 (Rel. 51) and the SWISS-PROT (Rel.34) databases
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| Molecular Sequence Megaclassification |
A server provides access to a non-redundant
molecular sequence collection that has been classified by
different research groups.
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| BLOCKS |
Multiply aligned ungapped segments corresponding to the most highly conserved
regions of proteins.
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| 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
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| 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.
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| HSSP |
A database of homology-derived secondary structure of proteins.
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| COG |
Clusters of Orthologous Groups (COGs) were delineated by comparing protein sequences
encoded in 8 complete genomes, representing 6 major phylogenetic lineages.
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| Structure Classfication |
| Dali/FSSP |
A network service for comparing protein structures in 3D.
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| SCOP |
Structural Classification of Proteins.
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| 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).
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| Genome |
| SGD |
A scientific database of the molecular biology and
genetics of the yeast Saccharomyces cerevisiae
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| YPD |
A protein database with emphasis on the physical and functional
properties of the yeast proteins.
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| MIPS |
The Yeast Genome database
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| Yeast Gene Duplications |
This Web site contains data on duplicated genes in the yeast (Saccharomyces cerevisiae) genome.
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| atDB |
Arabidopsis thaliana Genome Database
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| Haemophilus influenzae
|
Genome information for Haemophilus influenzae
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| FlyBase |
A Database of the Drosophila Genome
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| ACEDB |
A Database of the C. elegans Genome
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| MDG |
Mouse Genome Informatics
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| TIGR Microbial Database |
A listing of microbial genomes and chromosomes
completed and in progress
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| Human |
| GDB |
The official central repository for genomic mapping data
resulting from the Human Genome Initiative.
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| HGMD |
Human Gene Mutation Database
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| OMIM |
Online Mendelian Inheritance in Man.
A catalog of human genes and genetic disorders
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| CGAP |
An interdisciplinary program to establish the information and
technological tools needed to decipher the molecular anatomy
of a cancer cell.
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| GeneCard |
A database of human genes, their products and
their involvement in diseases.
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| HUGO |
Human Gene Nomenclature Committee
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| TGDB |
The Tumor Gene Database
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| Functions |
| WIT |
An environment for interpreting sequenced genomes for supporting metabolic reconstruction .
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| KEGG |
Kyoto Encyclopedia of Genes and Genomes
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| DIP |
Database of Interacting Proteins
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| 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.
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| signaling |
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| HIC-Up |
A reesource for structural biologists dealing with
hetero-compounds
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| ReliBase |
A database system for analysing receptor/ligand
complexes deposited in the Brookhaven Protein Databank.
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| Prediction |
| TMpred |
A program makes a prediction of membrane-spanning regions and their
orientation.
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| TMAP |
Transmembrane protein fragment prediction program
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| DAS |
Transmembrane protein fragment prediction program
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| SOUSI |
Transmembrane protein fragment prediction program
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| COILS |
Coiled coil fragment prediction program
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| Paircoil |
Coiled coil fragment prediction program
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| The PredictProtein server |
PHDsec, PHDacc, PHDhtm, PHDtopology, TOPITS, MaxHom, EvalSec
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| PREDATOR |
A secondary structure prediction
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| GOR IV |
A secondary structure prediction
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| NNPREDICT |
A secondary structure prediction
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| SSPRED |
A secondary structure prediction
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| 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.
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| Threader |
A threading protein structure prediction program
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| Swiss-Model |
An Automated Comparative Protein Modelling Server
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| MODELLER |
A program for homology protein structure modelling by satisfaction of spatial restraints.
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| Calculations |
| Peptide Mass |
Compute peptide Mass
|
| Compute pI/Mw tool |
Compute pI/Mw tool
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| Translate tool |
a tool which allows the translation of a nucleotide (DNA/RNA) sequence to a
protein sequence.
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| CLUSTALW |
A Multiple sequence align program
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| MSA |
A Multiple sequence align program
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| Multalin |
A Multiple sequence align program
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| ALIGN |
A Multiple sequence align program
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| AMAS |
A Multiple sequence align program
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| NCBI BLAST programs |
NCBI's sequence similarity search tool designed to support analysis
of nucleotide and protein databases.
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| GCG |
Software for the Analysis of Genes and Proteins
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| 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.
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| PSI |
Protein Structure Initiative Database. A database help selecting and tracking protein targets |
| PubMed |
A literature reference database
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| ENZYME |
A repository of information relative to the nomenclature of enzymes.
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| TUTORIAL |
Terry Gaasterland's TUTORIAL ON The Role of Computational Biology In High-Throughput Structure Determination
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