LINKS

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• Professor Drennan’s course Principles of Chemical Science added to MIT’s OpenCourseWare
• Professor Drennan featured at SBGrid consortium
• Professor Drennan’s iBioSeminar on Metalloproteins: Introduction, Medicine, and the environment
• Figures of molecules and/or electron density:
  • Examples of various formats with scripts
  • Introduction on making images using O with examples
  • See also Software two sections below
  • Stereo images using Molscript or Ribbons
• Interactive Structure Factor Tutorial
• International Union of Crystallography
• Multiple Anomalous Dispersion (MAD):
  • MAD theory and literature
  • Scaling of MAD data by Philip R. Evans
• Protein Stereochemistry Analysis:
  • Atlas of side-chain and main-chain hydrogen bonding
  • Papers: Good model-building and refinement practice
  • PARVATI from E.A.Merritt
  • Protein Structure Quality Score

Twinning:

• Bacteriorhodopsin
• Data Reduction from Twinned RNA Crystals (ACA abstract)
• SHELX97 also deals with twinning

PRESENTATIONS

• Poster presentation tips from Colin Purrington

DATABASES

• Cambridge Structure Database (CCDC)
• DALI (protein structure comparison)
• Database of Interacting Proteins (DIP)
• BRENDA Enzyme Database
• Heavy-Atom Databank
• ModBase – Database of comparative protein structure models
• Nucleic Acid Database
• Protein DataBank (PDB): <search>
• RELIBase (ligand search in PDB)

SOFTWARE

• CCP4; its wiki and its Newsletter; CCP4 bulletin board
• CHIME (web page interactive manipulation of macromolecules)Crystallography & NMR Software (CNS)
  • CNS_solve 1.3 (Yale University site)
• DPS-MOSFLM (Data Processing Suite from Purdue Univ.)
• ESPOIR (reverse Monte Carlo with powder diffr. data)
• FINDNCS – NCS finding from heavy atom sites
• Gimp
• ImageMagick
• MAR-Research & software
• Molscript
• MOSFLM and its user manual
• POVRAY
• Protein-Protein Interaction Server
• Rasmol
• Raster3D
• SHARP / BUSTER
• SOLVE
• Structure factor tutorial
• Swiss-PdbViewer Art Gallery

• XtalView

• XtalView Tutorials from Mike Sawaya

1. Setup
2. Native
3. Patterson Map
4. Anomalous Difference Patterson Map
5. Isomorphous Difference Patterson Map
6. Phasing, Density Modification, & Electron Density Map Calculation
7. Chi Squared Test with Isomorphous data
8. Chi Squared Test on Anomalous Data

• XV

– – – IUCr list of Software – – –

Books on Crystallography

Crystal Structure Analysis – Jenny Pickworth Gluster and Kenneth N. Trueblood – ISBN # 0-19-503531-3

Crystallography Made Crystal Clear – Gale Rhodes – ISBN # 0-12-587072-8

Crystallization of Nucleic Acids and Proteins – A. Ducruix and R. Giege’ – ISBN # 0-19-963245-6

Introduction to Crystallography – Donald E. Sands – ISBN # 0-486-67839-3

Methods in Enzymology Vol 114 Diffraction Methods for Biological Macromolecules – ISBN # 0-12-182015-7

Methods in Enzymology Vol 276 Macromolecular Crystallography, Part A – ISBN # 0-12-182177-3

Methods in Enzymology Vol 277 Macromolecular Crystallography, Part B – ISBN # 0-12-182178-1

Practical Protein Crystallography – 2nd Ed – Duncan E. McRee – ISBN # 0-12-486052-4

Principles of Protein X-Ray Crystallography – 2nd Ed – Jan Drenth – ISBN # 0-387-98587-5

Protein Crystallization: Techniques, Strategies, and Tips – Terese M. Bergfors – ISBN # 0-9636817-5-3

Symmetry and Structure – S. F. A. Kettle – ISBN # 0-471-90501-1 (Cloth) / ISBN # 0-471-90705-7 (Paperback)

The Development of X-Ray Analysis – Sir Lawrence Bragg – ISBN # o-486-67316-2

Theory of X-Ray Diffraction in Crystals – William H. Aachariasen – ISBN # 0-486-68363-X

Vectors and Tensors in Crystallography – Donald E. Sands – ISBN # 0-486-68505-5

X-Ray Diffraction – B. E. Warren – ISBN # 0-486-66317-5

X-Ray Diffraction in Crystals, Imperfect Crystals and Amorphous Bodies – A. Guiner – ISBN # 0-486-68011-8

SOME SYNCHROTRON RADIATION SOURCES

ALS (Berkeley)

CHESS (Ithaca)

DESY, Hasylab (Hamburg)

Elettra (Trieste)

EMBL-Hamburg

ESRF (Grenoble)

KEK (Tsukuba)

SPring-8 (Hyogo)

SSRL (Stanford)

• Synchrotron Beamlines for Macromolecular Crystallography

 

Biology / Genetics

 | Entrez | | ExPasy & SwissProt | N.C.B.I. | PubMed | | Material Safety Data Sheets | 

• Brutlag (Bioinformatics)
• Dana-Farber Cancer Institute Molecular Biology Core Facility
• EMBL-Heidelberg
• GCG manual
• Signal Transduction Knowledge Environment (part of Science online)
• Visual embryos

BACTERIA

• A Bacterial Primer
• American Type Culture Collection
• E. coli Genetic Stock Center
• E. coli Genome Center
• Salmonella Genetic Stock Center
• Who’s who amongst bacteria: (up-to-date)
  • Bacterial species nomenclature
  • List of bacterial names with standing in nomenclature

 

BIOCHEMISTRY

• E. coli metabolism
• Enzyme Datasheets:Wortington Catalog’sSWISS-PORT search

GENOMICS

• Camilla Kao web page with genomics links
• Comparative genomics:
  • Campylobacter jejuni
  • Corynebacterium diphtheriae NCTC 13129
  • Mycobacterium tuberculosis H37Rv
  • Pseudomonas Genome Project
• DNA microarray & Data analysis:
  • ArrayExpress Database
  • ATGC Consortium
  • ExpressDB Information Page (John Aach and Wayne Rindone, Harvard Univ.)
  • George Church lab (Harvard Med. School)
  • M-Guide: Pat Brown’s manual to build and use a microarrayer
  • Microarray & Data Analysis (Wentian Li, Rockefeller Univ.)
  • microarray.org
  • National Cancer Institute
  • Owen, Art (Reports, course descriptions etc)
  • Pat Brown’s lab (which includes the microarrayer)
  • Puces-ADN (Server at the CNRS, France)
  • Research Genetics
  • Seigel-C Protocols
• GeneCensus Genome Comparison
• Gene-Chips.com (DNA Microarrays)
• Sanger Sequencing Center

MOLECULAR BIOLOGY

• Codon usage of about 5000 organisms
• Dana-Farber Cancer Institute Molecular Biology Core Facility
• GCG manual
• Restriction Enzyme Database REBASE (New England Biolab):. Comprehensive Enzyme list

SEQUENCE ANALYSIS & PRESENTATION

• BOXSHADE (Presentation of sequence alignment)
• ExPasy and SwissProt
• Multiple Sequence Alignment
• National Center for Biotechnology Information (NCBI)
• ORF’s Finder at NCBI
• pI and M.W. (calculated)
• ProSAL (Protein Sequence Analysis Launcher)
• SeqAnalRef
• Deletion Project

YEAST

• Gene-Chips.com
• MicroArrayer at Pat Brown’s lab
• Saccharomyces Genome Database
• Yeast gene duplications

DATABASES SEARCHES

• ExPASy and SwissProt
• Litterature:
  • Entrez
  • Institute for Scientific Information (ISI) (Also look at Web of science (part of Science Citation Index))
  • PubMed
• Material Safety Data Sheets (searchable)
• National Center for Biotechnology Information (N.C.B.I.)
• Restriction Enzyme Database: Comprehensive Enzyme listwithin REBASE
• Web of science (part of Science Citation Index)

SOME SCIENTIFIC SOCIETIES

• American Association for the Advancement of Science
• American Cancer Society
• American Chemical Society
• American Society for Microbiology
• British Society for Antimicrobial Chemotherapy
• Canadian Federation of Biological Societies
• Federation of American Societies for Experimental Biology
• National Academy of Sciences
• Pittsburgh Diffraction Society