Molecular Biology


Cell and Molecular Biology Online - Protocols  
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
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
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
BioInformatics & Molecular Analysis Section (BIMAS)  
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
Cell and Molecular Biology Online  
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
Molecular Biology Jump Station  
A very useful collection of links for molecular biologists.
Submitted: Dec 08, 2000
Molecular Biology Shortcuts  
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
Molecular Modeling Heidelberg  
Offers free online services and tools for molecular modelling; focus is on carbohydrates.
Submitted: Oct 31, 2000
Antibody Resource Page  
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
KEGG Regulatory Pathways  
Graphical pathway maps, ortholog group tables, and molecular catalogs.
Submitted: Nov 19, 2000
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
Antibodies - Structure and Sequence  
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
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
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
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
Database of Interacting Proteins  
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
Enzyme Structures Database  
This database contains the known enzyme structures that have been deposited in the Brookhaven Protein Data Bank (the PDB).
Submitted: Nov 26, 2000
Guide to Cloned Glycosyltransferases  
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
IMB Jena Image Library  
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
Influenza Sequence Database  
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
Molecular Mining Corporation  
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
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
The BIOpolymer Markup Language (BIOML)  
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
The Department of Crystallography, Birkbeck College  
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
The Molecules of Life  
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
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
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
Database of Macromolecular Movements  
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
DNA Data Bank of Japan
Submitted: Sep 27, 2000
Enzyme Nomenclature  
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
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
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
Molecular Systematics  
Molecular Systematics and Evolution of Microorganisms. The Natural History Museum, London and Instituto Oswaldo Cruz, FIOCRUZ Rio de Janeiro, Brazil.
Submitted: Sep 26, 2000
NCBI Taxonomy Homepage  
Taxonomy resource description. Allow to browse taxonomy tree that contains classification of organizms.
Submitted: Nov 18, 2000
O-GLYCBASE is a database of O-glycosylated glycoproteins.
Submitted: Oct 22, 2000
Oligonucleotide Probe Database: OPD  
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
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
The Primer Generator  
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
UCLA-DOE Fold Recognition Server  
The UCLA-DOE Fold-Recognition server is a new project conceived by D. Fischer ( 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
The EMBL Nucleotide Sequence Database.
Submitted: Oct 08, 2000

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