Webb servers
Macromolecules and biology

Contents

• General interest
• Proteins
• Nucleic acids
• Other substances

General interest

• ABC Agricultural Biotechnology Center (Hungary), hungarian node of EMBnet
• AISOIA WEb site for Molecular Biology
• Antibody Resource Page
• BCM Search Launcher On-going project to organize molecular biology-related search and analysis services available on the WWW
• BioMagResBank Repository for Data on Proteins, Peptides, and Nucleic Acids from NMR Spectroscopy
• Bioperl association of developers of public domain Perl tools for computational molecular biology.
• Biosci BIOSCI is a set of electronic communication forums - the bionet USENET newsgroups and parallel e-mail lists - used by biological scientists worldwide.
• Biosci FAQ Frequently asked questions.
• Biosciences
• BioToolkit    Online molecular biology research tools for the analysis of

 nucleic acid and protein sequences, genome structure, and biomacromolecular structure
 and function.
• CEPH Genotype database Paris, France
• Collaborative BioMolecular Tools Presents a number of collaborative projects. (CBMT).
• Cytokines Web site, UK
• Deambulum An easy access into the jungle of biologic information from CITI2, Paris, France.
• DNA bend.it This server predicts bendability and propensity to curvature from DNA sequences.
• ECTOC Hyperglossary. A hyperglossary is essentially a database of terms cross-indexed to related and derived properties and presented on-screen as a hypertext document.
• Entrez NIH (US)
• Heavy atom databank
• ImMunoGeneTics Integrated information system specializing in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) and related proteins of the immune system of human and other vertebrate species.
• Ion channel  anonymous ftp site  for ion channel-related material
• MDPI Molecular Diversity Preservation International (MDPI), a nonprofit and an independent international organization coordinates and provides supporting services of worldwide registration, deposit and distribution of molecular and biomolecular samples for chemistry journals, for chemistry and biochemistry professionals and for commercial and academic organizations.
• mmCIF Macromolecular Crystallographic Information File
• The National Library of Medicine US
• General interest databases
• EMBnet databases
• GenoBase at NIH USA.
• Heidelberg EMBL
• Infobiogen Genome Database. French node of EMBnet.
• INFOBIOGEN Bio E-mail server

This mail server allows you to retrieve records by keyword searching (like the E-mail server at the NCBI), in dbEST, Genbank, Embl, Swissprot. These searchs can be process on the release or on the updates. To receive the instructions for use, you have just to send an E-mail to retrieve@infobiogen.fr with "datalib help" in the body. (bank = genbank embl or dbest)
• SRS at EBI (UK)
• SRS at CSC (Finland)
• Oligo server
• PCR Information and links on all aspects of the Polymerase Chain Reaction (PCR)
• Representation of Molecular Models A course in english or in french from the dept of Physical Chemistry, Geneva, Switzerland
• XPLOR Library of X-PLOR topology and parameter files for several hundred hetero compounds
• X-PLOR resources on Web
• X-PLOR archive list

Proteins

• AAA superfamily
• AUTODEP AutoDep Version 1.0 is a World Wide Web-based graphical interface to the deposition form which leads the author through the entire submission process.
• Brookhaven National Lab. US
information about the PDB.
• Chaperonin home page
• CSBS Cambridge School of Biological Sciences (UK)
• CARB at NIST (US)
• Cis-pro and Cis-peptides List from the PDB.
• DBGET Database Links Diagram Kyoto Japan
• ExPAsy Molecular Biology Server This server is dedicated to the analysis of protein and nucleic acid sequences as well as 2-D PAGE
• EU Protein Engineering & Structural Biology U. K. page of RTD Programmes in Europe
• GPSDB the Gene and Protein Synonym Database. The most comprehensive database of gene and protein name synonyms. This authoritative thesaurus, published by PharmaDM, has been compiled in cooperation with SIB (the publishers of Swiss-Prot and ExPASy), OFAI, the University of Manchester, and others.
• Heavy-atom databank Contains details of experimental conditions used for protein crystallization
• Klotho: Biochemical Compounds Declarative Database
• MMDB This database represents our effort to rebuild the Brookhaven PDB protein structure database into a new format using an ASN.1 based data specification. MMDB data files help to correct some of the inconsitencies in PDB data files.
• MOOSE Macromolecular Structure Query. MOOSE has its own internal database system which is synchronized with the contents of the PDB ftp server.
• NIH SwissProt + PIR + GenBank + PDB gateway at NIH(US)
• NRL -3D protein structure Database at John Hopkins U. USA
• O and X-PLOR dictionaries
• OBSTRUCT A service to obtain a largest non-redundant set of protein structures from PDB according to crystallographic resolution and sequence identity
• PDBReport Here you can find reports describing structural problems in PDB entries that have been determined using X-ray diffraction techniques.
• Prolysis Protease and protease inhibitor Web server
• Protein Data Bank (Infobiogen site in France)
• Protein Data Bank PDB files accessible by anonymous ftp (Infobiogen site in France)
• Protein Data Bank(Pasteur site in France)
• PDB transition plan from Brookhaven National laboratory (BNL) to the Research Collaboratory for structural bioinformatics (RCSB)
• Protein Side-Chain Interactions
• PDB select from EMBL Heidelberg. Representative list of protein data bank chain identifiers from U. Hobohm and C. Sander
• ProDom Protein Database Toulouse France
• Protein Sequence Analyzer U. of Boston. On-line program for Protein Sequence Analysis.
• PSdb The Protein Structure Database (PSdb), is a protein database, dervived from the information available in the Protein Databank and NRL-3D database, that relates secondary (e.g. Helix, Sheet, Turn, Random Coil) and tertiary information (e.g. Solvent accessibility, internal relative distances, and ligand interactions) to the primary structure.
• Ramachandran revisited About Ramachandran plots.
• SCOP Centre for Protein Engineering, Cambridge (UK)
• SCOP Structural Classification of Proteins
• TRANSFAC Library of protein binding sites contains more than 200 entries
• VRML browser for PDB macromolecules. Need a VRML browser.

Nucleic acids

• Nucleic Acid Database (NDB)
• Rütgers U., USA
• Europe
• Japan
• Webcutter On-line tool for restriction mapping nucleotide sequences

Other substances