Nano Science

FUTHER LINKS

WEB TOOLS

Literature

Biosci Includes a complete archive and searchable indexes of all bionet newsgroup postings, and some other usefull stuff.

Entrez With links to sequence and structure databases.

OED Online The online version of the Oxford English Dictionary

PudMed NLM's search service to access the 9 million citations in MEDLINE and Pre-MEDLINE (with links to participating on-line journals), and other related databases.

Sequence & structure retreval

BioMagResBank (BMRB) is the publicly-accessible depository for NMR results from peptides, proteins, and nucleic acids recognized by the International Society of Magnetic Resonance and by the IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy. In addition, BMRB provides reference information and maintains a collection of NMR pulse sequences and computer software for biomolecular NMR.

Entrez With links to literature.

PDB The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules.

PIR The Protein Identification Resource Protein sequence database.

SRS at EBI. Sequence Retrieval System Network Browser for Databanks in Molecular Biology. Contains all the databases you can think of!

SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotations (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc), a minimal level of redundancy and high level of integration with other databases.

The EMBL Nucleotide Sequence Database The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences collected from the scientific literature and patent applications and directly submitted from researchers and sequencing groups.

Sequence similarity search and alignment

BLAST Another really fast sequence similarity search!

DBWatcher a server for periodic BLAST searcher against sequence databases. You'll get the results in your e-mail!

Fasta Do a search and get the results in your e-mail

GeneFIND Family Identification System. Find the family to which your sequence belongs.

ITERALIGN v1.0 A program for the multiple alignment of protein sequences.

LOCK Hierarchial Protein Structure Superposition. A program that superimposes a query structure on top of a target structure.

Pfam Protein families database of alignments and Hidden Markov Models.

PRINTS A compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family

ProDom A The ProDom protein domain database consists of an automatic compilation of homologous domains detected in the SWISS-PROT database.

SCOP Structural Classification of Proteins, a databases of known structures, sorted according to structure.

Prediction tools

A long list maintained by the Center for Biological Sequence Analysis at DTU.

HMMTOP An automatic server for predict transmembrane helices and topology of proteins.

Jpred A consensus method for protein secondary structure prediction at EBI.

PHD The PredictProtein server (by Burkhard Rost). Predicts secondary structure, solvent accessibility and transmembrane segments.

PSIPRED Protein structure prediction. Contains PSIpred (secondary structure),MEMSAT (transmembrane) and GenTHREADER (Fold Recognition)

SWISS-MODEL An automated protein modelling server running at the GlaxoWellcome Experimental Research in Geneva, Switzerland. Gives a 3D model of your sequence.

TopPred2 Topology prediction of membrane proteins.

Structure validation

Biotech Validation Suite for Protein Structures web interface to Procheck, WhatIf & Prove

GETAREA 1.1 Computes surface areas and solvation energies for structures

Genetic stuff

CloneIt An ANSI-C program finding sub-cloning strategies, in-frame deletions and frameshifts using restriction enzymes and DNA polymerases.

Misc.

Atlas of Protein Side-Chain Interactions

Beilstein references for synthesis etc. of organic compounds.

GenomeNet a Japanese server with, among other things, biochemical pathways.

LIPIDAT a database with lipid thermodynamic properties & structures.

NMR knowledge base. Lots of news in the field of NMR.