MARTINDALE'S BIOSCIENCE & BIOTECHNOLOGY CENTER PROTEINS, AMINO ACIDS NUCLEIC ACIDS, ENZYMES, PEPTIDES, SNP COURSES, TEXTBOOKS, DATABASES, TUTORIALS, MOVIES

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ALL INCLUSIVE DATABASES (Swiss-Prot, SNP, ExPASy etc.) DATABASES BY SUBJECT Amino Acids | Calcium Binding Proteins Composite Protein Sequence Enzymes | Fingerprints | G Protein Immunogenetics - Immunology Ligands Mass Proteometry - Mass Spectrometry Metalloprotein | Motions of Proteins & Fold Recognition Nucleic Acids | Olfactory | Peptides | Protein Crystals Proteome Analysis | Secondary Structure | Side-Chain Interactions Thermodynamics for Proteins & Mutants

All Inclusive Databases

Function, Domains Structure, Identification etc. EMBL-EBI DATABASES & TOOLS - European Bioinformatics Insitute (EBI), European Molecular Biology Laboratory (EMBL), U.K. Multimedia Databases (Text & Images). "...There are more than 20 main stream database productions available from EBI. Each of these has submissions and free search services ranging from sequence scanning to full text retrieval as well as secure on-line submission and analysis of user owned data..." For more information see European Bioinformatics Insitute SWISS-PROT - ExPASy Molecular Biology Server, Geneva University Hospital and the University of Geneva Multimedia Databases (Text & Images). "SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotations (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc), a minimal level of redundancy and high level of integration with other databases." For more information see ExPASy Molecular Biology Server, Geneva University Hospital and the University of Geneva BIOINFO BANK - BioInfo Bank, Kyushu Institute of Technology, Japan Multimedia Databases (Text & Images). For more information see BioInfo Bank - Old address PÔLE BIO-INFORMATIQUE LYANNAIS (PBIL) - Laboratoire de Biométrie, Biologie Evolutive (Biometry and Evolutionary Biology), Institut de biologie et Chime des Protéines (Institute of Biology and Chemistry of Proteins), Lyon, France Multimedia Databases (Text & Images). Includes: Sequence databases access; Similarity searches; DNA sequence analysis; Protein sequence analysis; etc. For more information see Laboratoire de Biométrie, Biologie Evolutive or the Institut de biologie et Chime des Protéines SNP (SINGLE NUCLEOTIDE POLYMORPHISMS) DATABASE - The SNP Consortium Ltd. PROSITE - ExPASy Molecular Biology Server, Geneva University Hospital and the University of Geneva Multimedia Databases (Text & Images). "PROSITE is a method of determining what is the function of uncharacterized proteins translated from genomic or cDNA sequences." For more information see ExPASy Molecular Biology Server, Geneva University Hospital and the University of Geneva PROTEIN DATABASE - Protein Information Resource (PIR), a division of the National Biomedical Research Foundation Multimedia Databases (Text & Images). For more information see GeneFind or the Protein Information Resource (PIR) MUNICH INFORMATION CENTER FOR PROTEIN SEQUENCES (MIPS) - Munich Information Center for Protein Sequences (MIPS), Munich, Germany Multimedia Databases (Text & Images). Includes the: "PIR-International Protein Sequence Database; European Yeast Functional Analysis Program; European Sequencing of Arabidopsis thaliana; German Network for Functional Analysis in Yeast; etc..." PROTEIN STRUCTURE CLASSIFICATION (CATH) - C.A. Orengo, A.D. Michie, S. Jones, M.B. Swindells, D.T. Jones & J.M. Thorton, Biomolecular Structure and Modelling Unit, University College London, U.K. Multimedia Databases (Text & Images). For more information see Biomolecular Structure and Modelling Group Home Page or the Department of Biochemistry and Molecular Biology STRUCTURAL CLASSIFICATION OF PROTEINS (SCOP) - A. Murzin, S.E. Brenner, T.J.P. Hubbard & C. Chothia, MRC Laboratory of Molecular Biology and Centre for Protein Engineering, Cambridge, England Multimedia Databases (Text & Images). Structural Classification of Proteins begining with "top of the hierarchy; sequence homology search and keyword search". Experimentally determined Three-Dimensional Structures... PROTEIN DATA BANK BROWSE (PDB) - Research Collaboratory for Structural Bioinformatics (RCSB) Multimedia Databases (Text & Images). "The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules." For more information see Research Collaboratory for Structural Bioinformatics (RCSB) ARCHIVE OF OBSOLETE PDB ENTRIES - Authors H. Weissig and P. Bourne, National Laboratory for Computational Science & Engineering, SDSC Multimedia Databases (Text & Images). "This archive can be used to locate and analyse obsolete entries from the Brookhaven Protein Data Bank (PDB)."

Databases by Subject

Amino Acids AMINO ACID COMPOSITION - Pôle Bio-Informatique Lyannais (PBIL), Laboratoire de Biométrie, Biologie Evolutive (Biometry and Evolutionary Biology), Institut de biologie et Chime des Protéines (Institute of Biology and Chemistry of Proteins), Lyon, France "...a simple tool giving you the amino-acid composition of your protein, its mass (Da) and the theoretical molecular epsilon at 280nm..." For more information see Pôle Bio-Informatique Lyannais (PBIL); Laboratoire de Biométrie, Biologie Evolutive or the Institut de biologie et Chime des Protéines Calcium Binding Proteins EF-HAND CALCIUM BINDING PROTEINS DATA LIBRARY - Developed by M. Nelson, Walter Chazin's Laboratory, Vanderbilt University "The EF-Hand Calcium-Binding Data Library is an expanding collection of sequence, structural, and functional information about the EF-Hand superfamily of calcium-binding proteins." For more information see Program in Structural Biology Composite Protein Sequence OWL: COMPOSITE PROTEIN SEQUENCE DATABASE - University of Manchester Specialist Node of EMBnet "OWL is a non-redundant composite of 4 publicly-available primary sources: SWISS-PROT, PIR (1-3), GenBank (translation) and NRL-3D. " For more information see UMBER Enzymes ENZYME: ENZYME NOMENCLATURE DATABASE - ExPASy Molecular Biology Server, Geneva University Hospital and the University of Geneva, Geneva Switzerland For more information see ExPASy Molecular Biology Server Fingerprints PRINTS (Protein Motif Fingerprint Database) - University of Manchester Specialist Node of EMBnet, UK "PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family." For more information see UMBER PROTEIN PROSPECTOR - K. Clauser & P. Baker, Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, School of Pharmacy, UCSF For more information see Mass Spectrometry Facility; Department of Pharmaceutical Chemistry; School of Pharmacy or UCSF G Protein GPCRDP: G PROTEIN-COUPLED RECEPTORS (GPCRs) DATABASE - Centre for Molecular and Biomecular Informatics, University of Nijmegen, The Netherlands For more information see Centre for Molecular and Biomecular Informatics Immunogenetics - Immunology IMGT: THE INTERNATIONAL IMMUNOGENETICS DATABASE - Coordinator: Marie-Paule Lefranc, Laboratoire d'ImmunoGénétique Moléculaire, Université Montpellier II, CNRS, Montpellier, France "IMGT, the international ImMunoGeneTics database, is an integrated database specialising in Immunoglobulins (Ig), T-cell receptors (TcR) and Major Histocompatibility Complex (MHC) molecules of all vertebrate species." For more information see the Laboratoire d'ImmunoGénétique Moléculaire Ligands LIGAND DATABASE - Institute for Chemical Research, Kyoto University For more information see the GenomeNet Mass Proteometry - Mass Spectrometry PROTEIN PROSPECTOR - K. Clauser & P. Baker, Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, School of Pharmacy, UCSF For more information see Mass Spectrometry Facility; Department of Pharmaceutical Chemistry; School of Pharmacy or UCSF Metalloprotein MDB - METALLOPROTEIN SITE DATABASE & BROWSER - Department of Molecular Biology, Scripps Research Institute "...a database that aims to contain quantitative information on all the metal containing sites available from structures in the PDB distribution, as well as from in-houe (TSRI) structures." For more information see Metalloprotein Structure and Design Program or the Department of Molecular Biology Motions of Proteins & Fold Recognition 3D-PSSM: PROTEIN FOLD RECOGNITION - Structural Bioinformatics Group, Imperial College Center Bioinformatics, U.K. Multimedia Databases (Text & Images). "A Fast, Web-based Method for Protein Fold Recognition using 1D and 3D Sequence Profiles coupled with Secondary Structure and Solvation Potential Information..." For more information see Structural Bioinformatics Group MOLECULAR MOVEMENTS DATABASE - N. Echols, Bioinformatics Web Server, Department of Molecular Biophysics and Biochemistry, Yale University Multimedia (Text, Images & Movies). This database describes the motions that occur in proteins and other macromolecules (such as RNA). Associated with it are a variety of free software tools for structural analysis." For more information see the Bioinformatics Web Server Examples from over '100' Molecular Movements currently online include Motion in HIV-1 protease [hivprot] Motion in Lactate Dehydrogenase (LDH) [ldh] Other online Databases include Movie Gallery of Macromolecular Motions Nucleic Acids NUCLEIC ACID DATABASE - Department of Chemistry, Rutgers University Multimedia. "The following prepared reports summarize some key information about the structures contained in the NDB archive: Names of structures in the NDB archive; Primary citations for NDB structures; Summary of structure features; Cell dimensions; Protein/DNA complexes; t-RNA structures; Structures with bound drugs; Structures with modified phosphates; Structures with modified bases and Structures with mismatched base pairs". Examples from the 'Nucleic Acid Database' include The Atlas of Nucleic Acid Containing Structures NDB Archives Olfactory OLFACTORY RECEPTOR DATABASE - Sense Lab Project, Shepherd Lab., Yale University School of Medicine Multimedia Databases (Text & Images). For more information see the The SenseLab Project Peptides ACCURATE MASS & PEPTIDE MODIFICATION - A. Bohne-Lang, Molecular Modeling, Central Sectroscopy Department, German Cancer Research Center (DKFZ), Heidelberb, Germany "Help to unravel information encrypted in the deltamass value of accurate peptide masses. Deltamass is the post-decimal-point part of the accurate mass..." For more information see the Andreas Bohne-Lang's Home Page; Central Sectroscopy Department - Molecular Modeling or PEPTIDE MASS - ExPASy Molecular Biology Server, Geneva University Hospital and the University of Geneva "Calculate masses of peptides and their posttranslational modifications for a SWISS-PROT entry or for a user sequence." For more information see ExPASy Tools Menu or ExPASy Molecular Biology Server Protein Crystals HEAVY-ATOM DERIVATIVES OF PROTEIN CRYSTALS - S.A. Islam, D. Carvin, M.J.E. Sternberg & T.L. Blundell, Biomolecular Modelling Laboratory, U.K. "...we have collected information on the preparation and characterisation of HEAVY-ATOM derivatives of protein crystals." For more information see Biomolecular Modelling Laboratory Proteome Analysis HUMAN 2-D PAGE DATABASES FOR PROTEOME ANALYSIS - Danish Centre for Human Genome Research, Danish Cancer Society, Denmark Multimedia Database (Text & Images). "You can display protein names and information on specific protein spots by clicking on the image of thegel representing the 2-D gel map in which you are interested." For more information see the Danish Cancer Society Secondary Structure PROTEIN STRUCTURE PREDICTION - Analytical Biostatistic Section, LSB, DCRT, NIH "A protein secondary structure prediction algorithm based on a quadratic logistic model using logistic discriminant function methodology." For more information see Analytical Biostatistic Section, LSB, DCRT, NIH Side-Chain Interactions ATLAS OF PROTEIN SIDE-CHAIN INTERACTIONS - R. Laskowski, Biomolecular Structure and Modelling Group, University College London, London, England, U.K. Multimedia (Text & Images). "This atlas depicts how amino acid side-chains pack against one another within the known protein structures." For more information see the Structure and Modelling Group; Department of Biochemistry and Molecular Biology, University Collge of London, UK or the University Collge of London Thermodynamics for Proteins & Mutants PROTHERM: THERMODYNAMIC DATABASE FOR PROTEINS AND MUTANTS - BioInfo Bank, Kyushu Institute of Technology, Japan "...collection of numerical data of thermodynamic parameters such as Gibbs free energy change, enthalpy change, heat capacity change, transition temperature etc. for wild type and mutant proteins,..." For more information see the BioInfo Bank

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