WEB RESOURCES

FOR PROTEIN SCIENTISTS

PROTEINS WWW RESOURCES

Albumin data

Protein Databank

PDB Reports at EMBL: - Comprehensive report of errors in PDB files from the Sander group at Heidelberg.

Molecules R US Protein Data Bank via the NIH: - An especially convenient interface for accessing PDB data

PIR the Protein Information Resource from NBRF

- The PIR, maintained by the National Biomedical Research Foundation , is one of three collaborating data centers responsible for collecting, organizing, and distributing the PIR-International Protein Sequence Database. The Resource includes protein and nucleic acid sequence databases and software for protein identification and for retrieval of associated information.

Swiss-Prot an Annotated Protein Sequence Database from ExPASy: - Provides a high level of annotations such as: the description of the function of a protein, its domains structure, and post-translational modifications, variants, etc. There is a minimal level of redundancy and a high level of integration with other databases.

NCBI Structure Group at the NIH

- Included are links to NCBI's current use of MIME-types document, MMDB - Molecular Modelling DataBase (via WWW-Entrez from which you can get machine-verified, corrected PDB files at various levels of detail, and Kinemage rendered files from any PDB entry), MMDB's ASN.1 Specification documents, ASN.1 Resources (info and tutorials), and FTP sites for NCBI software and tool kit source code.

RasMol Molecular Visualization at the University of Massachusetts: - RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. The program has been developed at the University of Edinburgh's Biocomputing Research Unit and the Biomolecular Structure Department at Glaxo Research and Development, Greenford, UK.

GenBank at the National Center for Biotechnology Information: - Search MEDLINE, protein databases, and nucleotide databases using Entrez Browser with forms-based or non-forms based clients.

HIV Sequence Database at the Los Alamos National Laboratory: - The Human Retroviruses and Aids Database collects, curates, analyzes, and publishes genetic sequences of the human immunodeficiency virus (HIV) and related species. All HIV and related viral sequences and alignments are available via anonymous ftp at atlas.lan.gov in directory /pub/aids-db.

National Center for Genome Resources: - The Genome Sequence Data Base provides DNA sequence data retrieval and submission of nucleotide sequence data for the DDBJ, EMBL, GSDB, and NCBI databases. SIGMA, System for Integrated Genome Map Assembly, is a graphical database tool designed for building and viewing integrated genome maps.

Center for Biological Sequence Analysis: - A research site with a goal to obtain knowledge of the complex relations between sequence composition and macromolecular structure and function. The research is aimed at creating entirely new possibilities in the study of evolutionary processes by comparison of sequence patterns across species. The work of the center focuses in particular on a number of novel data driven and adaptive computational methods, which are not created on the basis of assumptions and known facts, but for example by training of artificial neural network algorithms.

Oxford Laboratory of Molecular Biophysics

- Access to Crystallographic Web Server and much more!

Principles of Protein Structure from Birkbeck College: - This is a course available on the Internet which is jointly sponsored by Birkbeck College and the Globewide Network Academy. The course uses a wide range of interactive and multimedia techniques to bring high-quality, low-cost learning to students throughout the world. The course is intended for scientists who need to know more about how and why protein structure is central to modern biology. The Protein Structure Course Announcement provides a course outline for committed scientists in disciplines such as chemistry, molecular biology, pharmacology, and immunology who wish to understand how the three-dimensional structures of proteins are critical to their functions.

BioMagResBank at University of Wisconsin-Madison

- BioMagResBank is supported by the NIH National Library of Medicine, contains the largest available repository of assigned NMR chemical shifts for proteins. Current aims are to expand the collection to all relevant NMR data from peptides, proteins and nucleic acids.

2-D PAGE Databases at the Danish Centre for Human Genome Research: - Contains data on proteins identified on various 2-D PAGE reference maps. You can display protein names and information on specific protein spots and search by protein name, SSP number or organelle or cellular component.

European Bioinformatics Institute (EBI): - EBI is an Outstation of the European Molecular Biology Laboratory. Links to the Human Genome Mapping Project and Nucleotide Sequence and several Protein Sequence Databases as well as Sequence Similarity Searches and Database query and retrieval are available.; - The most comprehensive enzyme information system worldwide including enzyme functional, structural, stability and other including links to other data bases.; - Literature and sequence databases of proteins and peptides since 1975. It includes biologically active peptides, chemistry of amino acids, peptides and proteins, primary structure of proteins, higher order structure of proteins, functional sites and motifs of proteins, and protein mutagenesis and mutational diseases.

VMD - Biololecular visualization software. VMD runs on many versions of Unix, Windows, and most recently MacOS-X.

GENERAL BIOLOGICAL WWW RESOURCES

BioMedNet

- An Internet membership club for researchers and clinicians in biology and medicine includes services such as: a full-text library of biomedical publications and databases, plus MEDLINE; conferencing facilities; notice boards and news; and a shopping mall. There is a free 1996 Test Membership. Included in the BioMedNet library are the following journals published by Current Biology Ltd.: Folding & Design Structure and Macromolecular Structures

University of Cambridge School of Biological Sciences

Pedro's BioMolecular Research Tools

- A huge collection of WWW links to information and services useful to molecular biologists. Visit the US, Germany, or Switzerland mirror sites.

European Molecular Biology Laboratory (EMBL): - Provides an online information service of activities at EMBL such as its scientific programs and the courses, conferences, and workshops given at EMBL.

OTHER USEFUL WWW RESOURCES

The Library of Congress: - Access to the Library of Congress WWW server

HyperDOC at the National Library of Medicine

Virtual Tourist II: - A map-based interface to City.Net, the Web's most extensive library of local and regional information. Provides general information, tourist guides, and pictures for thousands of places. "Virtually Tour" the world

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This document last updated: 4 December 2002

newburgh@protein.faseb.org