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.

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