| 3D Lectin Database
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The present database offers an extensive list of the known 3D-structures of lectins.
Submitted Nov 25, 2000
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| adh [adh]
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This page contains movies of protein motions.
Submitted Sep 16, 2000
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| Cell and Molecular Biology Online - Protocols
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This section of Cell and Molecular Biology Online lists online resources for cell and molecular biology research protocols. Most of the web sites focus on particular research techniques.
Submitted Nov 24, 2000
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| Antibodies - Structure and Sequence
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This page attempts to summarise useful information on antibody structure and sequence. It provides a query interface to the Kabat antibody sequence data, general information on antibodies and crystal structures and links to other antibody-related information.
Submitted Oct 19, 2000
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| Antibody Resource Page
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Find your antibody (and much more) with the ARP. There are links to online educational resources, companies, databases, journals, and more.
Submitted Nov 25, 2000
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| ATLAS
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The Atlas Retrieval System (ATLAS) is a mutlidatabase information retrieval program specifically designed to access macromolecular sequnece databases
Submitted Oct 24, 2000
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| BCM Search Launcher
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The Baylor College of Medicine Search Launcher is an on-going project to organize molecular biology-related search and analysis services available on the WWW by function by providing a single point-of-entry for related searches (e.g., a single page for launching protein sequence searches using standard parameters).
Submitted Nov 18, 2000
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| BEN
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BEN is the Belgian node of the EMBnet. It provides to scientific researchers in Belgium, both academic and industrial, an access to updated databanks with nucleic acid and protein sequences, as well as the necessary software to search these databanks and perform various sequence analysis tasks.
Submitted Nov 26, 2000
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| BIND
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BIND (Biomolecular Interaction Network Database) is a new database encompassing the growing network of protein and other biomolecular interactions. This database will span the complexity of interaction information gathered through experimental studies of biomolecular interactions. Interaction information will come from the literature, submitters and other databases.
Submitted Dec 02, 2000
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| Bio-Web
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Online resources for Molecular and Cell Biology: tools for sequence analysis, bio-journals, companies catalogues, protocols, web bio-directories, research institutions and other sites of biological interest.
Submitted Nov 24, 2000
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| BioInformatics & Molecular Analysis Section (BIMAS)
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Lots of computational tools and resources to unite advances in biology with those in computers, informatics, and networking for the genomic and genetic analysis fields of BioInformatics; division of the Computational Bioscience and Engineering Lab at the Center for Information Technology.
Submitted Nov 05, 2000
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| Biological Sequence Databases
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The list of Biological Sequence Databases: Protein and Amino Acid Databases, DNA and RNA Sequence Databases, Genomic Sequence Databases, and more.
Submitted Dec 08, 2000
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| BioToolKit
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The BioToolKit, an annotated directory of 1082 links to online molecular biology resources, includes basic research tools and advanced applications for genome, transcriptome, and proteome data retrieval, analysis, and visualization.
Submitted Sep 15, 2000
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| BMERC
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BioMolecular Engineering Research Center, specializing in Bioinformatics research, protein functional profiles, protein structure prediction, genome analysis and visualisations, and promoter analysis.
Submitted Nov 05, 2000
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| CATH
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CATH is 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). Class, derived from secondary structure content, is assigned for more than 90% of protein structures automatically. Architecture, which describes the gross orientation of secondary structures, independent of connectivities, is currently assigned manually.
Submitted Sep 20, 2000
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| Cell and Molecular Biology Online
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Cell and Molecular Biology Online, an informational resource for cell and molecular biologists. Features resources for biology research and education, including protocols, lab home pages, journals, grants, professional societies, conferences, career information, online courses and biological images.
Submitted Nov 24, 2000
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| Centraalbureau voor Schimmelcultures (CBS)
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The Centraalbureau voor Schimmelcultures is one of the world's largest service and research collections of filamentous fungi and yeasts. The collection comprises about 35,000 strains. Research of the CBS concentrates on taxonomy and phylogeny of selected groups throughout the Kingdom of Fungi.
Submitted Dec 01, 2000
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| Common Molecules
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X-ray Crystallography is one of the principal techniques for studying the structure of molecules and crystals. In the provided links, you can examine the structures of a variety of interesting molecules. Whenever possible, the data have been obtained from crystallographic sources, although some of the simple structures are calculated using molecular mechanics techniques.
Submitted Dec 17, 2000
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| Comprehensive Protocol Collection
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This resource attempts to offer a comprehensive collection of molecular biology and Nematode-related protocols. The site links to protocols either maintained directly by the Ambros Lab or at other locations around the world.
Submitted Dec 08, 2000
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| Database of Interacting Proteins
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This set of Web pages will allow you to: Search the DIP database (no password needed), To Submit new protein-protein interaction (registration required sent email to Webmaster), To update database entries either by adding new references to the DIP.
Submitted Sep 19, 2000
Updated Sep 27, 2000
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| Database of Macromolecular Movements
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This page contains gallery of movies of protein motions, along with software, including freeware for calculating volumes, surfaces, axes, angles, and distances.
Submitted Sep 16, 2000
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| DDBJ
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DNA Data Bank of Japan
Submitted Sep 27, 2000
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| Enzyme Nomenclature
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This page contains general information on enzyme nomenclature. It includes links to individual documents, and the number of these will increase as more sections of the enzyme list are revised. It also provides advice on how to suggest new enzymes for listing, or correction of existing entries.
Submitted Nov 19, 2000
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| Enzyme Structures Database
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This database contains the known enzyme structures that have been deposited in the Brookhaven Protein Data Bank (the PDB).
Submitted Nov 26, 2000
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| EpiMatrix MHC-Binding Prediction
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A site providing MHC-binding predictions for researchers working on vaccines and therapeutics for HIV and a range of other pathogens.
Submitted Dec 02, 2000
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| Guide to Cloned Glycosyltransferases
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This guide lists, and gives WWW links to sequence databases for: 1. Cloned eukaryotic glycosyltransferases involved in the biosynthesis of glycoproteins, glycolipids, glycosylphosphatidylinositols and other complex glycoconjugates (together with journal references); 2. Cloned prokaryotic glycosyltransferases involved in lipopolysaccharide biosynthesis; 3. Cloned glucuronyltransferases and some yeast chitin synthases (Swissprot links only).
Submitted Dec 02, 2000
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| HOMSTRAD
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The database defines homologous families and provides a structure-based alignment for the representative members of each family.
Submitted Sep 27, 2000
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| IMB Jena Image Library
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The IMB Jena Image Library of Biological Macromolecules is aimed at a better dissemination of information on three-dimensional biopolymer structures with an emphasis on visualization and analysis. It provides access to all structure entries deposited at the Protein Data Bank (PDB) or at the Nucleic Acid Database (NDB). In addition, basic information on the architecture of biopolymer structures is available.
Submitted Sep 15, 2000
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| ImMunoGeneTics Database
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IMGT, the international ImMunoGeneTics database, is a high-quality integrated database specialising in Immunoglobulins (Ig), T cell receptors (TcR) and Major Histocompatibility Complex (MHC) molecules of all vertebrate species, created in 1989 by Marie-Paule Lefranc (Université Montpellier II, CNRS).
Submitted Sep 27, 2000
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| Influenza Sequence Database
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The Influenza Sequence Database is a curated database of nucleotide and amino acid sequences. It is intended to provide the research community with easy sequence deposit and retrieval capabilities, together with tools tailored, in particular, to the analysis of hemagglutinin and neuraminidase sequences.
Submitted Nov 26, 2000
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| Interpreting Biological Sequences
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This site provides a comprehensive listing of all the major databases, web sites, and web suites available for sequence analysis.
Submitted Oct 24, 2000
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| KEGG Regulatory Pathways
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Graphical pathway maps, ortholog group tables, and molecular catalogs.
Submitted Nov 19, 2000
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| MatrixPlot
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MatrixPlot can be used to generate mutual information plots of sequence alignments, distance matrices of sequence with known 3D coordinates, and plots of user provided matrix files.
Submitted Dec 03, 2000
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| MHCPEP
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MHCPEP is a database comprising over 13000 peptide sequences known to bind MHC molecules. Entries were compiled from published reports as well as from direct submissions of experimental data. Each entry contains the peptide sequence, its MHC specificity and, when available, experimental method, observed activity, binding affinity, source protein, anchor positions, and publication references.
Submitted Dec 02, 2000
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| MICE
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SDSC's and NPACI's MICE project brings together resources from Molecular Sciences and Interaction Environments in a new approach to collaborative research and distance learning via the Internet.
Submitted Dec 17, 2000
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| ModBase
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A database of three-dimensional protein models calculated by comparative modeling.
Submitted Sep 20, 2000
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| Module
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GIF images that show the spread of the most abundant protein modules. For printing, these are also available as PostScript. This collection is maintained by Peer Bork.
Submitted Oct 19, 2000
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| MOE-Diffraction
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MOE's diffraction simulation application generates diffraction patterns for powder, single crystal, and fiber samples using three kinds of incident radiation under various camera settings. This article describes the basic principles of diffraction, and the diffraction simulation functionality provided in MOE.
Submitted Dec 23, 2000
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| Molecular Biology Jump Station
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A very useful collection of links for molecular biologists.
Submitted Dec 08, 2000
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| Molecular Biology Shortcuts
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The entry door to the Web for the Molecular Biologist. Molecular biology source of information (methods, tips, tools, software, databases...). On-line bio-tools.
Submitted Nov 24, 2000
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| Molecular Mining Corporation
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Specialized in the exploration, inference and prediction of molecular networks derived from gene expression, proteomics and SNPs (single nucleotide polymorphisms) data, and the application of these network models to diagnostic and drug target identification, predictive toxicology and in silico drug screening.
Submitted Nov 18, 2000
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| Molecular Modeling Heidelberg
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Offers free online services and tools for molecular modelling; focus is on carbohydrates.
Submitted Oct 31, 2000
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| Molecular Systematics
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Molecular Systematics and Evolution of Microorganisms. The Natural History Museum, London and Instituto Oswaldo Cruz, FIOCRUZ Rio de Janeiro, Brazil.
Submitted Sep 26, 2000
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| MSD
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The EBI Macromolecular Structure Database is the European Project for the collection, management and distribution of data about macromolecular structures.
Submitted Sep 27, 2000
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| NCBI Taxonomy Homepage
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Taxonomy resource description. Allow to browse taxonomy tree that contains classification of organizms.
Submitted Nov 18, 2000
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| NPS@
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NPS@ stands for Network Protein Sequence @nalysis. NPS@ is an interactive Web server dedicated to protein sequence analysis.
Submitted Nov 19, 2000
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| NWFSC Molecular Biology Protocols
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Molecular Biology Protocols at Microbial Pathogens Lab, Northwest Fisheries Science Center, National Oceanic & Atmospheric Administration.
Submitted Dec 08, 2000
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| O-GLYCBASE
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O-GLYCBASE is a database of O-glycosylated glycoproteins.
Submitted Oct 22, 2000
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| Oligonucleotide Probe Database: OPD
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OPD is a hyperlinked database of oligonucleotide sequences and associated experimental information which may be useful to scientists interested in using oligonucleotide probes in their research.
Submitted Nov 24, 2000
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| PDB Lite
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PDB Lite is designed for nonspecialists who search for atomic coordinate ("PDB") files at the Protein Data Bank on an occasional basis. It is especially targeted towards students and educators.
Submitted Dec 17, 2000
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| PRINTS
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PRINTS is 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 a SWISS-PROT/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours.
Submitted Sep 19, 2000
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| ProDom
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ProDom database was designed as a tool to help analyze domain arrangements of proteins and protein families. Strong emphasis has been put on the graphical user interface which allows for interactive analysis of protein homology relationships.
Submitted Sep 19, 2000
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| PROLYSIS
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PROLYSIS home page, intended as a Web resource for those interested in proteases and their natural or synthetic inhibitors. This page contains informations of general interest as well as useful links to other Internet resources.
Submitted Dec 02, 2000
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| Pronet
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This site contains information on protein-protein interactions that have been described in the published literature. Only interactions between human proteins that were identified using the two-hybrid system are included.
Submitted Sep 19, 2000
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| ProtoMap
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ProtoMap+ is an automatic hierarchical classification of all SWISSPROT and TrEMBL proteins.
Submitted Sep 19, 2000
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| PROWL
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This page is a navigation device, used to work through the Enzyme Commission database of known enzymes.
Submitted Nov 26, 2000
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| RefSeq
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The NCBI Reference Sequence project (RefSeq) will provide reference sequence standards for the naturally occurring molecules of the central dogma, from chromosomes to mRNAs to proteins. RefSeq standards provide a foundation for the functional annotation of the human genome. They provide a stable reference point for mutation analysis, gene expression studies, and polymorphism discovery.
Submitted Nov 18, 2000
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| SWISS-3DIMAGE
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SWISS-3DIMAGE (References) is an image database which strives to provide high quality pictures of biological macromolecules with known three-dimensional structure. The database contains mostly images of experimentally elucidated structures, but also provides views of well accepted theoretical protein models. The images are provided in several useful formats; both mono and stereo pictures are generally available.
Submitted Dec 03, 2000
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| SWISS-PROT
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SWISS-PROT is an annotated protein sequence database established in 1986 and maintained collaboratively by the Swiss Institute for Bioinformatics (SIB) and the European Bioinformatics Institute (EBI).
Submitted Sep 27, 2000
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| The BIOpolymer Markup Language (BIOML)
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This page is devoted to a new XML language, designed to be used for the annotation of biopolymer sequence information. BIOML allows the full specification of all experimental information known about molecular entities composed of biopolymers, for example, proteins and genes.
Submitted Nov 05, 2000
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| The Department of Crystallography, Birkbeck College
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The School of Crystallography is a multi disciplinary science research department studying the structure and function of macromolecules and industrial materials.
Submitted Dec 09, 2000
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| The MGuide
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The Brown Lab's complete guide to microarraying for the molecular biologist. DNA chips. Methods. Software.
Submitted Nov 25, 2000
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| The Molecules of Life
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An introduction to the techniques used to gain understanding of the structure of protein molecules. Includes x-ray crystallography and folding predictions.
Submitted Nov 25, 2000
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| The Primer Generator
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The Primer Generator is an automated generator of primers for site-directed mutagenesis. The program analyzes the original nucleotide sequence and desired amino acid sequence and designs a primer that either has a new restriction enzyme site or is missing an old one. This allows for faster sorting out of mutated and non-mutated sequences.
Submitted Nov 19, 2000
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| UCLA-DOE Fold Recognition Server
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The UCLA-DOE Fold-Recognition server is a new project conceived by D. Fischer (fischer@mbi.ucla.edu) aimed to help in the computational analysis and prediction of structure from amino acid sequences. This server provides easy access to the results of various programs. These include various methods developed in this lab, especially Fischer & Eisenberg's "Fold Recognition Using Sequence-Derived Predictions" (Protein Science, 5, 947-955, 1996), as well as other methods from around the world. Rather than a set of programs and hyperlinks, it is a comprehensive package providing users with computation time, storage and collection of data, and organization of the results for easy analysis. The server provides predictions for single sequences or for entire genomes.
Submitted Dec 09, 2000
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| UTRscan
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The program UTRscan looks for UTR functional elements by searching through user submitted sequence data for the patterns defined in the UTRsite collection.
Submitted Nov 19, 2000
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| VecScreen
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VecScreen is a system for quickly identifying segments of a nucleic acid sequence that may be of vector origin. NCBI developed VecScreen to combat the problem of vector contamination in public sequence databases. This web page is designed to help researchers identify and remove any segments of vector origin prior to sequence analysis or submission.
Submitted Nov 19, 2000
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| Virtual Genome Center
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The Virtual Genome Center is a place where molecular biologists can access tools and databases to do their work. The VGC has no director, staff, grant support, or corporate sponsors. It simply exists.
Submitted Nov 05, 2000
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| Webin
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The EMBL Nucleotide Sequence Database.
Submitted Oct 08, 2000
Updated Oct 09, 2000
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| WebMolecules
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An active, sponsor-supported site designed for the 3D visualization of molecules. The site contains over 200,000 3D molecular molecules. You can search the database by Formula, CAS or NSC Number, Common Name, or browse by category, formula, fragments, valences, or orbitals. The models can then be viewed in full 3D using a VRML or Chime plug-in.
Submitted Sep 16, 2000
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| WORLD-2DPAGE
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This page contains references to known 2-D PAGE database servers, as well as to 2-D PAGE related servers and services.x
Submitted Dec 09, 2000
Updated Dec 16, 2000
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| Wormpep
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You can search the database for protein entries, or for their corresponding "cDNA" (not containing any UTR's). Look for a protein using one of the following query strings: the CDS identifier of the sequence (e.g. ZK1058.3); the Wormpep accession number (e.g. CE01103); a locus name (e.g. soc-2); a keyword contained in the brief annotation (e.g. helicase); a TREMBL or Swiss-Prot accession number (e.g. SW:Q09435); or a protein_id (e.g. CAA88083.1). The "cDNA" has to be retrieved using its CDS identifier (e.g. AH6.2).
Submitted Sep 27, 2000
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