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. The program runs on UNIX and Windows NT/95/98/2000 and is freely available. [Information of the supplier]
BioMagResBank (BMRB) is the publicly-accessible depository for NMR results from peptides, proteins, and nucleic acids recognized by the International Society of Magnetic Resonance and by the IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy. In addition, BMRB provides reference information and maintains a collection of NMR pulse sequences and computer software for biomolecular NMR. Access to data in BMRB is free directly from its web site (URL http://www.bmrb.wisc.edu) and ftp site (ftp.bmrb.wisc.edu) and will remain so as public funding permits. The concept of a biomolecular NMR data bank was developed under a five-year research grant awarded to the University of Wisconsin-Madison from the National Library of Medicine, National Institutes of Health. ... [Information of the supplier]
Our goal: to understand protein folding, misfolding, and related diseases. Proteins are biology's workhorses -- its "nanomachines." Before proteins can carry out these important functions, they assemble themselves, or "fold." The process of protein folding, while critical and fundamental to virtually all of biology, in many ways remains a mystery. Moreover, when proteins do not fold correctly (i.e. "misfold"), there can be serious consequences, including many well known diseases, such as Alzheimer's, Mad Cow (BSE), CJD, ALS, Huntington's, Parkinson's disease, and many Cancers and cancer-related syndromes. You can help by simply running a piece of software. Folding@home is a distributed computing project -- people from throughout the world download and run software to band together to make one of the largest supercomputers in the world. Every computer takes the project closer to our goals. Folding@home uses novel computational methods coupled to distributed computing, to simulate problems millions of times more challenging than previously achieved. We have had several successes. You can read about them on our Science page, on our Awards page, or go directly to our Results page. ... [Information of the supplier, modified]
The p53 tumor suppressor gene was initially identified as being essential for the DNA damage checkpoint, but it was subsequently found to have a broader function after cellular stress, such as oncogene activation or hypoxia. The p53 protein functions as a tetrameric transcription factor found at very low levels in normal unstressed cells. After stress, different pathways lead to post-translational modification of the protein and its stabilization. p53 database contains 16,000+ entries corresponding to TP53 mutations found in tumors, normal skin, and noncancerous diseases such as rheumatoid arthritis. The database also includes germline mutations found in Li-Fraumeni syndrome (LFS) and LFS-like syndrome. ... [Information of the supplier, modified]
SWISS-2DPAGE is an annotated two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and SDS-PAGE database established in 1993 and maintained collaboratively by the Biomedical Proteomics Reasearch Group (BPRG) of the Geneva University and the Proteome Informatics Group of the Swiss Institute of Bioinformatics (SIB). The SWISS-2DPAGE database assembles data on proteins identified on various 2-D PAGE and SDS-PAGE maps. Each SWISS-2DPAGE entry contains textual data on one protein, including mapping procedures, physiological and pathological information, experimental data (isoelectric point, molecular weight, amino acid composition, peptide masses) and bibliographical references. In addition to this textual data, SWISS-2DPAGE provides several 2-D PAGE and SDS-PAGE images showing the experimentally determined location of the protein, as well as a theoretical region computed from the sequence protein, indicating where the protein might be found in the gel. Cross-references are provided to Medline and other federated databases. ... [Information of the supplier]
AACompIdent is a tool which allows the identification of a protein from its amino acid composition. It searches the Swiss-Prot and / or TrEMBL databases for proteins, whose amino acid compositions are closest to the amino acid composition given. [Information of the supplier]
This page allows you to test an antibody sequence against the Kabat sequence database. Any unusual residues (occurring in < 1% of chains in the database) will be reported to you. This allows the identification of potential cloning artifacts and sequencing errors. The current Kabat database contains 6014 light chains and 7895 heavy chains. ... [Information of the supplier]
CATH is a 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. The topology level clusters structures into fold groups according to their topological connections and numbers of secondary structures. The homologous superfamilies cluster proteins with highly similar structures and functions. The assignments of structures to fold groups and homologous superfamilies are made by sequence and structure comparisons. The boundaries and assignments for each protein domain are determined using a combination of automated and manual procedures. These include computational techniques, empirical and statistical evidence, literature review and expert analysis. ... [Information of the supplier]
DOLOP provides information for several hundred lipoproteins with relevant links to molecular details. Features include functional classification, predictive algorithm for query sequences, primary sequence analysis and lists of predicted lipoproteins ... [Information of the supplier, modified]
The membrane organization and subcellular location of a protein can provide information about its functional role. Historically, these data have been difficult to produce on a large scale for higher eukaryotic organisms. However, recent advances in membrane organization prediction methods and high-throughput subcellular localization assays have made it possible to generate these datasets. LOCATE is a curated, web-accessible database that houses data describing the membrane organization and subcellular localization of proteins from the FANTOM3 Isoform Protein Sequence set. Membrane organization is predicted by the high-throughput, computational pipeline MemO. The subcellular locations of selected proteins from this set were determined by a high-throughput, immunofluorescence-based assay and by manually reviewing over 1700 peer-reviewed publications. The results of the MemO pipeline and the subcellular localization methods are stored in the database with supporting information including a graphical depiction of the membrane organization juxtaposed with InterPro-predicted features and links to several external databases. The database is searchable by subcellular location, protein class, descriptive keyword, and sequence similarity. The data are retrievable in human- and machine-readable formats and in batch. ... [Information of the supplier]
