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Useful Links

RESOURCES:
Biomedical Information
    EPAS
    GENBANK
    HCGB
    PUBMED
    Will Ray
   

  Journals
    ACS
    CELL
    NATURE
    SCIENCE
    

Crystallography Tools
    BOBSCRIPT
    CCP4
    CNS
    CRYSTAL101
    HAD
    HKL
    IUCR
    O
    PDB
    PHASES
    SHARP
    SOLVE
    USF
    XPLOR
    SCATTERING
   

Synchrotron Radiation Research
    APS
    SSRL
    BNL

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Resources for Molecular Biology Information:

Expert Protein Analysis System (expasy.org)

 Proteomics server of the Swiss Institute of BioInformatics (SIB) dedicated to the analysis of protein sequences and structures 

Genbank (www.ncbi.nlm.nih.gov/Genbank)

Sequence submission support & software (including sequence similarity search tool, BLAST; submission tools, BANKLT and SEQUIN; and vector contamination screening tool, VECSCREEN).

Human Center Genetics Bioinformatics (pandora.med.ohio-state.edu)

Site of the Ohio State Genomics and Bioinformatics containing links to other human genome resources

PubMed (www.ncbi.nlm.nih.gov/PubMed)

National Library of Medicine search service - provides access to citations in MEDLINE, PreMEDLINE, other related databases, and links to participating online journals.

Will Ray's BIoInformatics Tools (www.biosci.ohio-state.edu/~ray/) 

Web site of Will Ray at OSU, containing links to other Bioinformatics softwares and systems

Resources for journal/publication search:

ACS Publications (pubs.acs.org)

Link to the American Chemical Society Publications Division, which published or co-published over 30 magazines and peer-reviewed journals. The Division also publishes research materials in print and on the Web. Citation info. for articles is available free of charge prior to their hardcopy publication via ACS's ASAP Alerts service.

Cell (www.cell.com)

Links to published research papers in CELL, (archive contains issues as far back as May 1,1974 - summaries only), IMMUNITY, NEURON, and MOLECULAR CELL.

Nature (www.nature.com)

Links to the Nature Publishing Group, which is comprised of the journals: NATURE, NATURE GENETICS, NATURE MEDICINE, NATURE CELL BIOLOGY, NATURE BIOTECHNOLOGY, NATURE IMMUNOLOGY, NATURE NEUROSCIENCE, and NATURE STRUCTURAL BIOLOGY. This site also contains a directory of scientific events throughout the year, a link to postgraduate and professional grants available in the scientific field worldwide, and the NATURE GENOME GATEWAY, which is a web resource devoted to genomics.

Science (www.sciencemag.org)

Links to publications across all areas within the scientific field. This site also contains the funding database, GRANTSNET.

Resources for Crystollography tools:

Bobscript (orval.rega.kuleuven.ac.be/~robert/bobscript) - a package of computer programs for the Phases manuals, which are used to compute phase angles for diffraction data for macromolecule crystals. 

CCP4 (www.dl.ac.uk./CCP/CCP4/main.html) - a collection of disparate programs covering most of the computations required for macromolecular crystallography.

CNS - Crystallography & NMR System (cns.csb.yale.edu) - a program that provides a flexible multi-level hierarchical approach to macromolecular structure determination, including heavy atom searching, experimental phasing (including MAD and MIR), density modification, crystallographic refinement with maximum likelihood targets, and NMR structure calculation using NOEs, J-coupling, chemical shift, and dipolar coupling data.

Crystallography 101
(www-structure.llnl.gov/xray/101index.html) - a comprehensive introduction to X-ray crystallography, covering experimental setups to model building. 

HAD - Heavy Atom Databank (www.bmm.icnet.uk/had/heavyatom.html) - a databank that contains information on: experimental conditions for crystallization; chemical details of the heavy-atom compounds used; bibliographic references; atomic coordinates of heavy-atoms; details of binding sites of heavy-atoms/protein crystal environment; and atomic coordinates of heavy-atoms/protein crystal environment.

HKL (www.hkl-xray.com) - software and hardware solutions for X-ray crystallography laboratories and synchrotron beam lines.

IUCR (www.iucr.org/welcome.html) - a web of crystallography services, including Crystallography Journals Online: Acta Cryst. A, Acta Cryst. B, Acta Cryst. C, Acta Cryst. D, J. Appl. Cryst, and J. Synchrotron Rad; the "International Tables for Crystallography" online, and SINCRIS (Information Exchange for Crystallography).

O Resources (origo.imsb.au.dk/~mok/o) - for users of the O protein crystallographic package.

PDB - Protein Data Bank (www.rcsb.org/pdb) - the single international repository for the processing and distribution of 3-D macromolecular structure data primarily determined experimentally by X-ray crystallography and NMR.

Phases (imsb.au.dk/~mok/phases/phases.html#toc2) - a package of computer programs for the Phases manuals, which are used to compute phase angles for diffraction data for macromolecule crystals. 

Sharp - Statistical Heavy-Atom Refinement & Phasing
(babinet.globalphasing.com/) - operates on data from SIR(AS), MIR(AS), and MAD experiments.

SOLVE (www.solve.lanl.gov) - Automated crystallographic structure solution for MIR and MAD.

USF - Uppsala Software Factory (xray.bmc.uu.se/usf)

XPLOR (xplor.csb.yale.edu/xplor-info) - a system for x-ray Crystallography & NMR for computers. Main focus is the three-dimensional structure determination of macromolecules using crystallographic diffraction or nuclear magnetic resonance (NMR) data.

X-Ray Anomalous Scattering (brie.bmsc.washington.edu/scatter) - a tool for crystallographers considering MAD data collection, and may be of some use to those considering the use of spectroscopy (XAFS, DAFS) or small-angle scattering.

Resources for Synchrotron Radiation Research

APS - Advanced Photon Source (www.aps.anl.gov) - a national synchrotron radiation (insertion-device- and bending-magnet-based) research facility located at Argonne National Laboratory near Chicago, Illinois.

SSRL - Stanford Synchrotron Radiation Laboratory (www.slac.stanford.edu) - a national user facility at Stanford University, Palo Alto, CA, that provides synchrotron radiation used to investigate objects of atomic and molecular size.

NSLS - National Synchrotron Light Source (www.nsls.bnl.gov) - a national user research facility at Brookhaven National Laboratory, Upton, NY that provides intense focused light spanning the electromagnetic spectrum from the infrared through x-rays and the specially designed experimental stations, called beamlines, for scientists to perform experiments not otherwise possible at their own laboratories.

 

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