Animated Dictionnary Definition

Mole

The amount of pure substance containing the same number of chemical units as there are atoms in exactly 12 grams of carbon-12 (i.e., 6.023 X 10²³).

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2Can Support Portal: This site provides short and concise introductions to basic concepts in molecular and cell biology and bioinformatics. The main emphasis is placed on making it as easy as possible for the user to understand which tools and databases are available from the EBI and from sites belonging to its collaborators
A quick introduction to elements of biology - cells, molecules, genes, functional genomics, microarrays: This is a brief introduction to molecular biology with emphasis on genomics and bioinformatics. It is intended for scientists, engineers, computer programmers, or anybody with background or strong interest in science, but without background in biology, and first of all for those joining the EBI . On one hand we have tried to distil the content down to the absolute minimum needed to make some sense of bioinformatics, while on the other to leave in enough to show why it is interesting.
A Visit With Dr. Francis Crick (Access Excellence classic collection): What follows is a transcript of a visit with Dr. Francis Crick, co-discoverer of the structure of the DNA molecule. Dr. Crick offers a fascinating look at the world of science at the time of this important discovery, as well as an equally fascinating glimpse into the thought processes of a brilliant scientist and thinker.
Algorithms for Phylogenetic Reconstructions: These lecture notes are the result of a series of lectures given by Martin Vingron (MPI/FU Berlin) and Jens Stoye (Bielefeld University) and a practical course by Hannes Luz (MPI, Berlin). As the title implies, the focus of these notes is on ideas and algorithmic methods that are applied when evolutionary relationships are to be reconstructed from molecular sequences or other species related data. Biological aspects like the molecular basis of evolution or methods of data acquisition and data preparation are not included. (PDF)
Amino Acid Repository (the): The IMB Jena Image Library of Biological Macromolecules contains visual and other information on three-dimensional biopolymer structures.
BCM Search Launcher :: The BCM Search Launcher organizes and simplifies molecular biology-related search and analysis services available on the WWW. It provides a single point-of-entry for related services, for example, a single page for launching nucleic acid sequence searches using standard parameters. See last newsletter
BEAUty and BEAST: BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It is not intended solely as a method of reconstructing phylogenies but also as a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.
Biochemical Learning Resource: These are a growing collection of educational resources for students of Biochemistry produced by Jon Maber in the Department of Biochemistry & Molecular Biology of The University of Leeds..
Biochemistry programs: These programs can be useful to biochemists. (one that helps locating molecules and enzymes in the metabolsim network, chemical calculator...)
Bioedit Tutorial: BioEdit is, among other things, an alignment editor, although it has many more capabilities. It is available free from the Department of Molecular Biology at North Carolina State University.
BioMolecular Engineering Research Center: The BMERC is using and creating tools and methods for the study of computational biology. The center is working on secondary protein structure prediction, providing reliable profiles, and developing new ways to study molecular biology through Bioinformatics. Our work has led to the formulation and testing of major hypotheses in the areas of molecular evolution, gene regulation, developmental genetics, and protein structure-function relationships.
Bioresearch online: Source for professionals in the bioresearch and life sciences industry- Information on drug discovery, laboratory systems and equipment, molecular and cell biology, genetic sequencing and more
BioToolKit (The): The restructured and updated BioToolKit, [***] an annotated directory of over 900 links to online molecular biology and neuroinformatics resources, includes basic research tools as well as advanced tools enabling integrated, multi-level analysis of the genome, transcriptome, and proteome.
CCMS Home Page: The Computational Center for MacroMolecular Structures (CCMS) . The Computational Center for Macromolecular Structure (CCMS) is distributing and supporting software for the determination and analysis of the structures of biological macromolecules.
ChromDB: The Plant Chromatin Database: The mission of ChromDB is to bring together information on homologs of chromatin-associated proteins encoded by plant genomes, organize this information logically and in a comparative manner across species (with reference to other eukaryotes to the extent possible), and make it readily accessible to any members of the research and teaching communities who might be interested in the role played by chromatin proteins in the control of gene expression and genome organization. Our first priority is to provide (a) complete sets of genes encoding chromatin-associated proteins (CAPs) for those plant species with complete or near-complete genome sequences (currently Arabidopsis and rice, with poplar to be displayed in the future), (b) the best available splicing models and predicted protein sequences for these genes, and (c) a molecular phylogenetic context for understanding the evolutionary diversification of these protein families during plant evolution with reference to animal and fungal homologs. Our next priorities will be to identify and present CAP genes in all available EST and partial genomic sequences of other plant species, as well as to provide information regarding their biochemical, developmental, physiological, and cellular functions through a community annotation mechanism.
Cis-Peptide Bonds in Proteins: The IMB Jena Image Library of Biological Macromolecules contains visual and other information on three-dimensional biopolymer structures. It provides access to all structure entries deposited at the Protein Data Bank (PDB) or at the Nucleic Acid Database (NDB).
Compute pI/Mw: is a tool which allows the computation of the theoretical pI (isoelectric point) and Mw (molecular weight) for a list of SWISS-PROT and/or TREMBL entries or for a user entered sequence [reference].
Cybergene: Quality, reliable, and affordable molecular biology services including: Oligo synthesis, DNA sequencing, Genotyping, Bioinformatics, etc.
Cytoscape: Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. Cytoscape is available as a platform-independent open-source Java application, released under the terms of the LGPL.
Deep View Tutorial (SPDB viewer): This tutorial provides an introduction to macromolecular modeling with Deep View, including review of many basic concepts in protein structure.
Deoxy-Ribonucleotides and Watson-Crick Basepairs: The IMB Jena Image Library of Biological Macromolecules contains visual and other information on three-dimensional biopolymer structures. It provides access to all structure entries deposited at the Protein Data Bank (PDB) or at the Nucleic Acid Database (NDB).
Discovery Studio Visualization: Gain insight into the potential implications of your molecule\'s structure by using Discovery Studio Visualization tools to simultaneously view its molecular data from multiple perspectives.
DNA ligase (pdb - molecule of the month): DNA ligase reconnects DNA strands when they are broken. It uses a cofactor molecule (shown in red) for power and a special lysine amino acid (shown in magenta) to perform the reaction.
DNA ligation protocol: DNA ligation is the process of joining together two DNA molecule ends (either from the same or different molecules). Specifically, it involves creating a phosphodiester bond bond between the 3\' hydroxyl of one nucleotide and the 5\' phosphate of another. This reaction is usually catalyzed by a DNA ligase enzyme. This enzyme will ligate DNA fragments having blunt or overhanging, complementary, \'sticky\' ends. Typically, it is easier to ligate molecules with complementary sticky ends than blunt ends. T4 DNA ligase is the most commonly used DNA ligase for molecular biology techniques and can ligate \'sticky\' or blunt ends.
EMBOSS on Codequest (BAB web server): EMBOSS is The European Molecular Biology Open Software Suite. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages.
Enzymatic RNA Molecules and the Replication of Chromosome Ends: A cell must orchestrate thousands of chemical reactions in order to live, to grow, and to respond to its environment. These chemical reactions rarely happen spontaneously but are usually catalyzed by macromolecules called enzymes. It was long thought that all enzymes were proteins. More recently we and others have found that RNA can in some cases act as an enzyme.
Flybase: FlyBase is a database of genetic and molecular data for Drosophila. It is available through FlyBase servers, as partial mirrors on other servers, as flat files, and as printed text (in special issues of Drosophila Information Service). The full database includes data files, documents, indices, forms, and images and is maintained on a multi-protocol server that supports a variety of tools and formats.
Genamics JournalSeek: Genamics JournalSeek is a database of molecular biology, microbiology, biochemistry, and general biology journals which are available (in whole or in part) through the internet. All information is fully searchable by various criteria. The database presently contains more than 360 different titles, and is growing rapidly.
Genamics SoftwareSeek: Genamics SoftwareSeek is a respository and database of freely-distributable and commercial tools for use in molecular biology and biochemistry.
IMB Jena Image Library of Biological Macromolecules: The IMB Jena Image Library of Biological Macromolecules contains visual and other information on three-dimensional biopolymer structures. It provides access to all structure entries deposited at the Protein Data Bank (PDB) or at the Nucleic Acid Database (NDB). In addition, general information on the architecture of biopolymer structures is available.
IMGT - International ImMunoGeneTics Database: 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. IMGT includes two databases : LIGM-DB, a comprehensive database of Ig and TcR from human and other vertebrates and MHC/HLA-DB (in development). A tool, IMGT/DNAPLOT, will allow Ig, TcR and MHC sequence analysis.
IMGT, international ImMunoGeneTics database: 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). IMGT, a European project since 1992, works in close collaboration with EBI.
Internet Tutorial in Biochemistry and Biophysics: Biomolecular Structures: Biomolecular Structures is an Internet tutorial intended as a computer-based laboratory exercise for undergraduate students in basic biochemistry.
Introduction to Protein Structure: This project develops, tests and incorporates into introductory chemistry and biology courses a series of modules based on important scientific themes: molecular aspects of biological structures, bonding and intermolecular forces, dynamics including enzymes and catalysis, aspects of equilibria especially acids and bases, energy and thermodynamics, organic reaction mechanisms especially metabolism, and bioethics.
Invitrogen BioInformatics Central: Invitrogens new portal is the nexus from which you can access our comprehensive suite of bioinformatics tools for molecular biology. Keep up-to-date with our new releases here.
Java based Molecular Biologist's Workbench: The programs and documentation that you will find hereby enclosed had been put together in order to try to give a free access to the exploitment of the most common bioinformatic operations that a molecular biologist currently has...
Journal of Molecular Biology: The Journal of Molecular Biology publishes original scientific research concerning studies of organisms or their components at the molecular level. Published weekly, the journal provides up-to-date and comprehensive coverage of all aspects of molecular biology.
KEGG: Kyoto Encyclopedia of Genes and Genomes: A grand challenge in the post-genomic era is a complete computer representation of the cell, the organism, and the biosphere, which will enable computational prediction of higher-level complexity of cellular processes and organism behaviors from genomic and molecular information. Towards this end we have been developing a bioinformatics resource named KEGG as part of the research projects of the Kanehisa Laboratories in the Bioinformatics Center of Kyoto University and the Human Genome Center of the University of Tokyo.
Kimball's Biology Pages: Meiosis: The pages consist of alphabetized lists of biological terms (a glossary) mostly from the areas of molecular and cellular biology. Many items are linked to "mini" essays on the topic.
Kimball's Biology Pages: Mitosis: The pages consist of alphabetized lists of biological terms (a glossary) mostly from the areas of molecular and cellular biology. Many items are linked to "mini" essays on the topic.
Mega: the goal of the MEGA (Molecular Evolutionary Genetics Analysis) software project has been to make useful methods of comparative sequence analysis easily accessible to the scientific community for research and education.
MetaDB: A Metadatabase for the Biological Sciences: The MetaDB metadatabase is a sorted, searchable collection of biological databases. Most entries in the metadatabase include a relevant peer-reviewed abstract or excerpt along with a link to the abstract or full text article. Database descriptions surrounded by quotation marks were borrowed from the database websites. Descriptions that include neither quotation marks nor an abstract were written by MetaDB\'s director, Shawn Thomas. Many of the category names included in MetaDB were borrowed from the NAR Molecular Biology Database Collection, which is maintained by Michael Y. Galperin of the National Center for Biotechnology Information (NCBI).
Molecular Biology Freeware for Windows: A list of molecular biology freeware
Molecular Biology Gateway: The ultimate gateway to Web resources for molecular biology, genetics, microbiology, and biochemistry
Molecular Genetics: The objectives of the course were, and continue to be: to train students to interpret experimental observations in molecular genetics; to have students understand the experimental bases for molecular genetic principles; and to train students to apply experimental methods of molecular genetics to problems in that science. These objective have been shaped by my philosophy of teaching science. I believe it more important that students learn why we believe the things we believe about molecular genetics than to memorize current hypotheses of the the science.
Molecular Genetics: Chromosomes: The three conceptual types of chromosomes, their interrelation and inheritance.

The objectives of the course were, and continue to be: -to train students to interpret experimental observations in molecular genetics;
-to have students understand the experimental bases for molecular genetic principles; and
to train students to apply experimental methods of molecular genetics to problems in that science.
Molecular Visualization Freeware (Rasmol) Email list: This email list is for discussion of RasMol, Chime, Protein Explorer, and other molecular visualization software (especially of the free variety)
MolMol: MOLecule analysis and MOLecule display: MOLMOL is a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR.
Monod, Jacques Lucien: To George Teissier he owes a preference for quantitative descriptions; André Lwoff initiated him into the potentials of microbiology; to Boris Ephrussi he owes the discovery of physiological genetics, and to Louis Rapkine the concept that only chemical and molecular descriptions could provide a complete interpretation of the function of living organisms.
NCBI: National Center for Biotechnology Information: Established in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease.
OmniMapFree: OmniMapFree is a computer program for displaying and analysing the genome of any organism. You can use it to generate genome maps of your own favourite organism and to link chromosome, genetic, transcriptomic, proteomic, molecular mutant and many other types of important information directly to the genomic sequence. It is very easy to use - it does not require any knowledge of databases or computer programming. All of the data is held in plain text files which can be created and modified using a simple text editor e.g. Notepad or Wordpad.
On Gaps: Gonzalo Giribet andWard C. Wheeler, Molecular Phylogenetics and Evolution Vol. 13, No. 1, October, pp. 132143, 1999
Organic and fatty acids.: Organic acids are very important compounds in living things. First they are important components of structural molecules such as phospholipids and are an important source of energy.
Orion Molecular Services: Orion Molecular Services is a newly established Biotechnology company based in the state-of-the-art facilities of the Biosciences Incubator in Manchester, UK
Pedro's Molecular Biology Tools: Loads of Biomolecular databases.
Phi-base: Pathogene Host interaction: This database contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions
Phylemon: a suite of web-tools for molecular evolution, phylogenetics and phylogenomics
Phylogenetic Resources: Today\\\'s session is a VERY brief introduction to phylogenetics. For a more complete experience, consider the two week course, Workshop on Molecular Evolution held by the Marine Biological Laboratory at Woods Hole.
PhylOgenetic Web Repeater (POWER): The PhylOgenetic Web Repeater (POWER) allows users performing phylogenetic analysis with molecular data by most programs of PHYLIP package repeatedly. POWER provide two pipelines to process the analysis. One of them includes multiple sequence alignment (MSA) at the begining of the pipeline whereas the other begin phylogenetic analysis with aligned sequence.
Phylogeny.fr: Phylogeny.fr is a free, simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences.

Phylogeny.fr runs and connects various bioinformatics programs to reconstruct a robust phylogenetic tree from a set of sequences.
PLoS Biology: PLoS Biology features works of exceptional significance in all areas of biological science, from molecules to ecosystems, including works at the interface with other disciplines, such as chemistry, medicine, and mathematics.All works published in the PLoS Biology are open access. Everything is immediately available without cost to anyone, anywhere to read, download, redistribute, include in databases, and otherwise use subject only to the condition that the original authorship is properly attributed. Copyright is retained by the author
Primer on Molecular Genetics: Primer on Molecular Genetics
Primer3: Primer3 is a widely used program for designing PCR primers (PCR = Polymerase Chain Reaction). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers. PCR is used for many different goals. Consequently, primer3 has many different input parameters that you control and that tell primer3 exactly what characteristics make good primers for your goals.
Professor Richard J Cherry: The ability of cell surface receptors to move in the plane of the membrane and to form dynamic associations with themselves and with other cell surface molecules is of fundamental importance to many cellular functions. My research group has developed novel methods, based on fluorescence microscopy, for studying these properties. The instrumentation consists of a cooled slow-scan CCD camera attached to an
Protein Architecture tutorials: The Lehninger 3D Structure Tutorials are designed to accompany Principles of Biochemistry, 3rd edition, by Lehninger, Nelson, and Cox. They are built around the Chemscape Chime 2.0 plugin, which reads the atomic coordinates of a biological macromolecule and renders it as a fully interactive 3D structure.
Learn about all aspects of protein structure, from the chemical properties of the amino acids to the interaction of multiple chains in giant molecules.
Protein Data Bank Docs: The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules, serving a global community of researchers, educators, and students.
Protein Explorer: Protein Explorer is free software for visualizing the three-dimensional structures of protein, DNA, and RNA macromolecules, and their interactions and binding of ligands, inhibitors, and drugs. It is arguably the easiest-to-use software of its kind.
Protocol Online: Protocol Online (POL), formerly Shortcuts to Molecular Biology Protocols, provides researchers with comprehensive collection of links to cell and molecular biology, immunology protocols, methods and tips.
ProtParam: (References) is a tool which allows the computation of various physical and chemical parameters for a given protein stored in SWISS-PROT or for a user entered sequence. The computed parameters include the molecular weight, theoretical pI, amino acid composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY)
PubMed: he PubMed search system provides access to the PubMed database of bibliographic information, which is drawn primarily from MEDLINE and PREMEDLINE. In addition, for participating journals that are indexed selectively for MEDLINE, PubMed includes all articles from that journal, not just those that are included in MEDLINE. Finally, PubMed also provides access to the molecular biology databases included in NCBI's Entrez retrieval system. It is expected that access to additional National Library of Medicine databases will be added in the future.
QuickGene: QuickGene is a molecular biology program for DNA analysis, assembly and cloning - QuickGene Single User License 295.00
Rasmol: V2.6 Molecular Visualisation Program . RasMol2 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. RasMol runs on Microsoft Windows, Apple Macintosh, UNIX and VMS systems.
RESearch - a new computer program for DNA analysis: The main design philosophy behind the development of RESearch was to make the basic DNA analysis tools readily available on IBM PCs, and to make them easy to use. RESearch enables molecular biologists to analyse a GCG formatted sequence in several ways including searching for short nucleotide sequences and restriction enzyme sites, translating open reading frames and searching for short amino acid sequences.
Roundwood Park School: We are situated on the edge of Harpenden, a town of just under 30,000 people, which is about 25 miles north of London. Collaborate with IACR Rothamsted on the Molecular Biology Notebook project.'
Saccharomyces genome database: SGD is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast.
SCIENCE AND PLANTS FOR SCHOOLS: SAPS works with teachers and scientists to develop new resources to promote and support lively and interesting classroom work in plant science and molecular biology.
Scottish Crop Research Institute: SCRI aims to increase knowledge in the basic biological sciences; to improve crop quality and utilisation by the application of conventional and molecular genetical techniques and novel agronomic practices; and to develop environmentally benign methods of protecting crops from depredations by pests, pathogens and weeds.
Serial Cloner: Serial Cloner is a Molecular Biology software. It provides tools with an intuitive interface that assists you in DNA cloning, sequence analysis and visualization.
SRS Sequence Retrieval System : 5.: Network Browser for Databanks in Molecular Biology
STING: Sequence To and withIN Graphics: STING is a WWW tool for the simultaneous display of information about macromolecular structure (in STING's Graphics Frame) and sequence (in STING's Sequence Frame). Special attention is given to MacroMolecular INTERFACE analysis.
SWISS-MODEL: An Automated Comparative Protein Modelling Server: SWISS-MODEL is a fully automated protein structure homology-modeling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer). The purpose of this server is to make Protein Modelling accessible to all biochemists and molecular biologists World Wide.
The 1989 Nobel Prize in Chemistry: This yearŽs Nobel Prize in chemistry has been awarded to Sidney Altman, USA and Thomas Cech, USA for their discovery that RNA (ribonucleic acid) in living cells is not only a molecule of heredity but also can function as a biocatalyst.
The Draft Human Genome Sequence, an Introduction: Anyone with a computer and an Internet connnection can now explore the draft sequence of the human genome. How can molecular biologists capitalize on these data riches, and what are the advantages of using the assembled draft sequence? This website aims to jump-start those who want make use of this information, but are not sure where or how to start.
The Electrophoresis Society: The Electrophoresis Society Homepage: Improving and Promoting Technologies for Biomolecular Separation and Detection
The Molecules of Life: "The Molecules of Life" is an interactive document which explains the background to the work done in the Laboratory of Molecular Biophysics at the University of Oxford. It is intended to be accessible to a wide, non-specialist audience including young people of school age. Members of the Laboratory are invited to expand and amend the document but should remember that the purpose of this document is to expand the public understanding of science!
The Structure of a Transmembrane Channel: A research report of SCIENCE magazine ("The structure of the potassium channel: Molecular basis of K+ conduction and selectivity," by Doyle et al, SCIENCE, 280: 69-77, 1998) has shown the potassium channel in great detail. These researchers, working in New York City, solved the structure of the potassium channel from a bacterium using X-ray crystallography.
Tribolium Home Page: This site contains data and articles about the genetics of the red flour beetle, Tribolium castaneum, and related species. Work being done in Dr. Beeman's laboratory involves both standard and molecular approaches.
Twenty Amino Acids: The following list gives these notations along with hypertext references to download amino acid gif images and also interactive molecules.
VectorDB: VectorDB contains annotations and sequence information for many vectors commonly used in molecular biology. Information for more than 2600 vectors is available with search facilities. Vectors which are also in GenBank have direct links to that database via NCBI\'s Entrez browser!
VectorNTI Yahoo group: A user group for the Molecular Biology suite Vector NTI Advance, by Informax. This group is not affiliated with Informax, Inc. or Invitrogen. We are an independent users group. Please join and contribute or just see what you can learn by watching the action!
WHATIF: WHAT IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc.
Wilkins, Maurice Hugh Frederick: The discovery of the well-defined patterns led to the deriving of the molecular structure of DNA. Further X-ray studies established the correctness of the Watson-Crick proposal for DNA structure.

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The Molecular Biology Notebook Online
A Beginners' Guide to Molecular Biology

Mole

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The Molecular Biology Notebook OnlineA Beginners' Guide to Molecular Biology

Mole

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The Molecular Biology Notebook Online
A Beginners' Guide to Molecular Biology