Application Index

A collection of useful resources for Biomedical, Bioinformatics, and Structural Biology

This database describes the motions that occur in proteins and other macromolecules, particularly using movies. Associated with it are a variety of free software tools and servers for structural analysis.
View Application Entry for Database of Macromolecular Movements

BioMagResBank (BMRB) database is a Repository for Data from NMR Spectroscopy on Proteins, Peptides, and Nucleic Acids.
View Application Entry for BioMagResBank (BMRB)

BioMedNet is a website for biological medical researchers. It allows users to search and view articles from Elsevier Science publisher. Membership to BioMedNet is free, and members can search all of BioMedNet without charge. However, viewing full-text articles from publishers often requires payment or a subscription.
View Application Entry for BioMedNet

LIPIDAT is a relational database of thermodynamic and associated information on lipid mesophase and crystal polymorphic transitions. There are 19,959 records in LIPIDAT. The database includes lipid molecular structures. Currently the database consists mainly of glycero-and sphingolipids.
View Application Entry for LIPIDAT

Atlas of Protein Side-Chain Interactions depicts how amino acid side-chains pack against one another within the known protein structures. This packing, which is governed by the interactions between the 20 different types of side-chains, determines the structure, function, and stability of proteins.
View Application Entry for Atlas of Protein Side-Chain Interactions

The Whitehead Institute for Biomedical Research is a non-profit, independent research and educational institution with pathfinding programs in cancer and AIDS research, structural biology, genetics, infectious disease research, developmental biology, and transgenic science.
View Application Entry for Whitehead Institute for Biomedical Research

The Biophysical Society is a professional organization with nearly 7,000 members in the US and more than 45 countries. The Society encourages development and dissemination of knowledge in biophysics through its journal, Biophysical Journal, the Annual Meeting, smaller Discussions workshops, subgroups, newsletter, and outreach program conducted by Society committees.
View Application Entry for Biophysical Society

The European Molecular Biology Laboratory (EMBL) was established in 1974 and is supported by sixteen countries including nearly all of Western Europe and Israel. EMBL consists of five facilities, the main Laboratory in Heidelberg (Germany), Outstations in Hamburg (Germany), Grenoble (France) and Hinxton (the U.K.), and an external Research Programme in Monterotondo (Italy). EMBL was founded with a four fold mission: to conduct basic research in molecular biology, to provide essential services to scientists in its Member States, to provide high level training to its staff, students, and visitors, and to develop new instrumentation for biological research. Over its 25 year history, the Laboratory has had a deep impact on European science in all of these areas. EMBL has achieved so much because it is a truly international, European institution, because it has achieved a critical mass of services and facilities which are driven by cutting-edge biological research, and because it regards education at all levels as a way of life. The Laboratory has a number of unique features. Its Outstations provide European biologists access to large instruments for the study of protein structures, some of the worlds oldest and biggest databases of DNA and protein sequences, and a host of services operated by highly trained biologists who are simultaneously involved in their own research. The Outstations are optimally located on campuses which foster links to a much larger network of European science neighbors including the Sanger Centre and the Welcome Trust, DESY, the ESRF and the ILL, EMMA, and a host of academic and industrial partners.
View Application Entry for European Molecular Biology Laboratory (EMBL)

The Institute for Genomic Research (TIGR) Databases are a collection of curated databases containing DNA and protein sequence, gene expression, cellular role, protein family, and taxonomic data for microbes, plants and humans.
View Application Entry for The Institute for Genomic Research (TIGR)

GeneDis is a human genetic disease database with a user graphical interface to a seqence search engine. GeneDis currently includes 12 human genetic diseases. Known mutations are incorporated in the gene and protein sequences using hyperlinks. The 3D structure is presented in cases where it has been determined experimentally and/or in cases where a homology model can be built based on a template of known 3D structure.
View Application Entry for GeneDis (Human Genetic Disease Database)

The CATH database is a hierarchical domain classification of protein structures in the Brookhaven protein databank. All non-protein, model, and "C-alpha only" structures are not classified in CATH. Only crystal structures solved to resolution better than 3.0 angstroms are considered, together with NMR structures. This filtering of the Brookhaven databank is performed using the program SIFT (Michie et al, (1996)). There are four major levels in this hierarchy; Class, Architecture, Topology (fold family) and Homologous superfamily. Each level is described below, together with the methods used for assigning structures to a specific family.
View Application Entry for CATH (Protein Structure Classification)

The Protein Data Bank(PDB) is the single worldwide archive of structural data of biological macromolecules.
View Application Entry for Protein Data Bank (PDB)

The Nucleic Acid Database (NDB) is a project which assembles and distributes structural information about nucleic acids. It maintains the mmCIF Web site. (macromolecular Crystallographic Information File(mmCIF) is the IUCr-approved data representation for macromolecular structures.)
View Application Entry for Nucleic Acid Database (NDB)

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.
View Application Entry for SWISS-PROT (Protein Sequence Database)

Nearly all proteins have structural similarities with other proteins and, in some of these cases, share a common evolutionary origin. The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of all known protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification.
View Application Entry for Structural Classification of Proteins (SCOP)

3Dee contains structural domain definitions for all protein chains in the Protein Databank (PDB) [EBI-MSD/RCSB] that have 20 or more residues and are not theoretical models. In addition, the domains have been clusterd on sequence similarity and structural similarity. The resulting families are stored as a hierarchy.
View Application Entry for 3 Dee (Database of Protein Domain Definitions)

SWISS-MODEL is an Automated Protein Modelling Server developped at the GlaxoSmithKline in Geneva, Switzerland. The purpose of this server is to make Protein Modelling accessible to all biochemists and molecular biologists World Wide. The present version of the server is 3.5 and is under constant improvement and debugging. In order to help us refine the sequence analysis and modelling algorithms, please report of possible bugs and problems with the modelling procedure.
View Application Entry for SWISS-MODEL

The ExPASy (Expert Protein Analysis System) proteomics server from the Swiss Institute of Bioinformatics (SIB) is dedicated to molecular biology with an emphasis on data relevant to proteins. It allows you to browse through a number of databases produced in Geneva, such as SWISS-PROT, PROSITE, SWISS-2DPAGE, SWISS-3DIMAGE, ENZYME, CD40Lbase and SeqAnalRef, as well as other cross-referenced databases (such as EMBL/GenBank/DDBJ, OMIM, Medline, FlyBase, ProDom, SGD, SubtiList, etc). It also allows access to many analytical tools for the identification of proteins, the analysis of their sequence and the prediction of their tertiary structure. ExPASy also offers you many documents relevant to these field of research and you will find from the servers, links to most relevant sources of information across the Web.
View Application Entry for ExPASy (Expert Protein Analysis System)

PROSITE is a database of protein families and domains. It is based on the observation that, while there is a huge number of different proteins, most of them can be grouped, on the basis of similarities in their sequences, into a limited number of families. Proteins or protein domains belonging to a particular family generally share functional attributes and are derived from a common ancestor. It is apparent, when studying protein sequence families, that some regions have been better conserved than others during evolution. These regions are generally important for the function of a protein and/or for the maintenance of its three- dimensional structure. By analyzing the constant and variable properties of such groups of similar sequences, it is possible to derive a signature for a protein family or domain, which distinguishes its members from all other unrelated proteins. A pertinent analogy is the use of fingerprints by the police for identification purposes. A fingerprint is generally sufficient to identify a given individual. Similarly, a protein signature can be used to assign a newly sequenced protein to a specific family of proteins and thus to formulate hypotheses about its function. PROSITE currently contains signatures specific for about a thousand protein families or domains. Each of these signatures comes with documentation providing background information on the structure and function of these proteins.
View Application Entry for PROSITE (Database of protein families and domains)

PRESAGE is a collaborative resource for structural genomics. It provides a database of proteins, each of which has a collection of annotations reflecting current experimental status, structural assignments models, and suggestions. PRESAGE is a tool for scientists to keep track of structural knowledge of their proteins of interest.
View Application Entry for PRESAGE (collaborative resource for structural genomics)

The Dali server is a network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank. A multiple alignment of structural neighbours is mailed back to you. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. If you want to know the structural neighbours of a protein already in the Protein Data Bank, you can find them in the FSSP database.
View Application Entry for Dali (protein structure comparison)

Fold classification based on Structure-Structure alignment of Proteins (FSSP) database is based on exhaustive all-against-all 3D structure comparison of protein structures currently in the Protein Data Bank (PDB). The classification and alignments are automatically maintained and continuously updated using the Dali search engine.
View Application Entry for Fold classification based on Structure-Structure alignment of Proteins (FSSP)

MaxSprout is a fast database algorithm for generating protein backbone and side chain co-ordinates from a C(alpha) trace. The backbone is assembled from fragments taken from known structures. Side chain conformations are optimized in rotamer space using a rough potential energy function to avoid clashes.
View Application Entry for MaxSprout

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. The IMB Jena Image Library intends to fulfill both scientific and educational needs.
View Application Entry for IMB Jena Image Library of Biological Macromolecules

The RNA World Website at IMB Jena is a resource which lists Internet links on RNA related topics.
View Application Entry for RNA World Website

National Center for Biotechnology Information(NCBI) is a national resource for molecular biology information. NCBI develops new information technologies to aid in the understanding of fundamental molecular and genetic processes that control health and disease. More specifically, the NCBI has been charged with creating automated systems for storing and analyzing knowledge about molecular biology, biochemistry, and genetics; facilitating the use of such databases and software by the research and medical community; coordinating efforts to gather biotechnology information both nationally and internationally; and performing research into advanced methods of computer-based information processing for analyzing the structure and function of biologically important molecules.
View Application Entry for National Center for Biotechnology Information (NCBI)

European Bioinformatics Institute (EBI) is a centre for research and services in bioinformatics. The Institute manages databases of biological data including nucleic acid, protein sequences and macromolecular structures.
View Application Entry for European Bioinformatics Institute (EBI)

Biomedical Initiative at Pittsburgh Supercomputing Center (PSC)is an NIH sponsored high-performance computing resource for the biomedical community.
View Application Entry for Biomedical Initiative at Pittsburgh Supercomputing Center (PSC)