• Cambridge Structure Database (CCDC)
• DALI (protein structure comparison)
• Databases for Modeling
• Database of Interacting Proteins (DIP)
• EC Enzyme Database
• Heavy-Atom Databank
• Intein database server (at NEB)
• ModBase - Database of comparative protein structure models
• Molecular Structures Database (free until Sep. 1, 1999)
• Nucleic Acid Database
• PROMISE (Prostetic groups and metal ions in protein active sites)
• Protein DataBank (PDB): <search>
  • Detailed transition plans to Rutgers University
  • Documentation and Information
  • ftp to PDB (archives)
  • How to link to a specific PDB entry
  • Molecules R US (at the NIH)
  • Molecular Biology Servers, Databases, and Web Sites of Interest
  • Obsolete PDB entries (Useful!!)
  • Processing status of entries 'ON HOLD'
  • Search Lite
  • Submit data to PDB (AutoDep Input Tool)
  • Validation server (AdIt)
• RELIBase (ligand search in PDB)

• AC3D Modeller and its manual
• Alscript 2.0 and some examples
• ARP Refinement Program
• Babel
• Bobscript
• CCP4; its FAQ; its manual (also in PDF format) and its Newsletter; Scala v.2.7.1 (Jan. 2000)
• CHIME (web page interactive manipulation of macromolecules)
• Crystallography & NMR Software (CNS)
  • CNS_solve 0.9 (Yale University site)
  • Obtaining CNS
• DENZO and SCALEPACK from HKL Research
• DINO surface rendering like GRASP
• DPS-MOSFLM (Data Processing Suite from Purdue Univ.)
• ESPOIR (reverse Monte Carlo with powder diffr. data)
• FINDNCS - NCS finding from heavy atom sites
• Gimp
• GLRF reference manual
• GRASP or this additional site
• ImageMagick
• INSIGHT (which includes DELPHI)
• MAR-Research & software
• Molscript
• MOSFLM and its user manual
• O:
  • Main resources:
    | T.A.Jones | M.Kjeldgaard | G.Kleywegt |
  • Background colour and more by Mark Harris in Uppsula
  • Ball-interface for O
  • Essential commands
  • Extract a sphere of atoms (script)
  • FAQ
  • Figures etc..
  • Manual
  • Mouse Function Keys (O 6.2)
  • Newsgroup archive
  • O version 7.0 !
  • OPLOT 1.15 ftp site
  • Resources by M. Kjeldgaard
  • Space groups symmetry operators (230 space groups)
• Pine and Pico
• POV4GRASP (POVRAY rendering with GRASP)
• POVRAY and its manual
• Povscript (from Dan Peisach) and manual (use it with POVRAY)
• Protein-Protein Interaction Server
• Rasmol
• Raster3D
• Rayscript
• Rayshade
• Replace which includes GLRF, TF and ANGCAL (from L. Tong)
• Setor
• Shake and Bake and its anonymous ftp site nexus.hwi.buffalo.edu
• SHARP / BUSTER
• SHELX 97-2
• SOLVE
• SPOCK surface rendering (use it with raster3d)
• Strategy (manual page)
• Structure factor tutorial
• Swiss-PdbViewer Art Gallery
• TNT
• Uppsula Software Factory:
  | DEJAVU | RAVE | VOIDOO | X-UTIL |
  | MOLEMAN | MAPMAN | OOPS | SPASM or SPASM-ftp |
  • Dept Molecular Biology (Uppsala)
  • Documentation for available softwares
  • Environment variables used for RAVE and other programs
  • HIC-UP Hetero-compound Information Centre
  • Tutorials
• VMD
• X-PLOR
  • A.T.Brunger's Lab
  • Department Store
  • manual (ver. 3.1)
  • Resources
  • Topology and Parameter library
• XRayView
• XtalView
• XV

Crystals and Crystal Growing - Alan Holden and Phylis Singer - Lib of Congress # 60-5932
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

ALS (Berkeley) APS (Argonne) CHESS (Ithaca) DESY, Hasylab (Hamburg) Elettra (Trieste) EMBL-Hamburg ESRF (Grenoble) LURE (Orsay)

KEK (Tsukuba) MAXLab (Lund) NSLS (Brookhaven) SPring-8 (Hyogo) SRS (Daresbury) SSRL (Stanford)



• NSLS newsletter
• SDSC site on synchrotron facilities
• Synchrotron Beamlines for Macromolecular Crystallography

| Biology Benchwork | BLAST | Entrez |
| ExPasy & SwissProt | IMAGE | N.C.B.I. | PubMed |
| Material Safety Data Sheets | Genomes-Entrez |

• BiologyWeek newsletter
  from the Whitehead Institute for Molecular Research
• Biosciences at Harvard
• Brutlag (Bioinformatics)
• Centrifuges: rotor calculation
  (rpm and × g calculation for a great variety of rotors)
• CNN Science & Technology
• Dana-Farber Cancer Institute Molecular Biology Core Facility
• Electron micrographs of organisms (the Nanoworld Image Gallery)
• EMBL-Heidelberg
• Eukaryotic organelle genomes (e.g. mitochondria)
• GCG manual
• Molecular Virology at the University of Wisconsin
• Owl database search
• Pedro's BioMolecular Reasearch
• Roaches and cockroaches
• Signal Transduction Knowledge Environment (part of Science online)
• Visual embryos

• American Type Culture Collection
• E. coli Genetic Stock Center
• E. coli Genome Center
• E. coli Index (a lot about this bacteria)
• E. coli Open Reading Frames (very large tables)
• Microbial Underground
• Salmonella Genetic Stock Center
• Sites with extensive links
• Veterinary bacteriology - Dictionary (French)
• Who's who amongst bacteria: (up-to-date)
  • Bacterial species nomenclature
  • List of bacterial names with standing in nomenclature

• E. coli metabolism
• Enzyme Datasheets:
  Wortington Catalog's
  SWISS-PORT search
• Metabolic Pathways (Washington University, DC)
• Pathways: glycogen & glucose (animated glycolysis)
• Protein-Diseases Database
• Protein Kinase Resource

• Camilla Kao web page with genomics links
• Comparative genomics:
  • Bacillus subtilis genome server
  • Campylobacter jejuni
  • Corynebacterium diphtheriae NCTC 13129
  • Helicobacter pylori 26695
  • Helicobacter pylori J99
  • Mycobacterium tuberculosis H37Rv
  • Pseudomonas Genome Project
  • Pyrococcus furiosus and this additional site
• Deborah Schegg's Homepage
• DNA microarray & Data analysis:
  • Albert Einstein College of Medicine
  • ArrayExpress Database
  • ATGC Consortium
  • Autoscan 1.0
  • Clustering Analysis (by M. Eisen, Stanford Univ.)
  • Cornell Univ. site (by Andreas Matern)
  • European Bioinformatic Institute
  • ExpressDB Information Page (John Aach and Wayne Rindone, Harvard Univ.)
  • George Church lab (Harvard Med. School)
  • GRID IT (Viginia Tech / NC State)
  • M-Guide: Pat Brown's manual to build and use a microarrayer
  • Microarray Analysis (Supplement to Aug. 6, 99 issue of Science)
  • Microarray Centre - Ontario Cancer Institute
  • Microarray & Data Analysis (Wentian Li, Rockefeller Univ.)
  • microarray.org
  • National Cancer Institute
  • National Genome Research 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
  • Silicon Genetics
  • Stanford DNA Microarray Database
  • Stanford MicroArray Database
• GeneCensus Genome Comparison
• Gene-Chips.com (DNA Microarrays)
• Microbial genomics discussion group
• Sanger Sequencing Center
• TIGR Microbial Genome Database (completed and in progress)
• University of Oklahoma Advanced Center for Genome Technology

• BioCatalog (molecular biology softwares)
• Codon usage of about 5000 organisms
• Dana-Farber Cancer Institute Molecular Biology Core Facility
• GCG manual
• Intein database server (at NEB)
• Plasmid DNA prep
• Restriction Enzyme Database REBASE (New England Biolab):
  . Comprehensive Enzyme list
• Vector Database at ATCG

• AMAS - sequence alignment server by G. Barton; see also this page
• BLAST from N.C.B.I.
• BMERC - the PSA protein structure prediction server (Boston University)
• BOXSHADE (Presentation of sequence alignment)
• CATH - Protein structure classification
• ExPasy and SwissProt
• Motif search (Stanford University)
• 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
• Splice site finder
• Threader

• Deletion Project and its search page
• Gene-Chips.com
• GeneStorm from Invitrogen
• Introns
• MicroArrayer at Pat Brown's lab and Botstein's Lab
• Survey on microarray technology
• Molecular Physiology of CNS development
• Proteome Database
• Saccharomyces Genome Database and its search SGD page
• Yeast gene duplications
• Yeast Lab Homepages
• Yeast WWW virtual library

• Computer Retrieval of Information on Scientific Projects (C.R.I.S.P.)
• ExPASy and SwissProt
• Litterature:
  • CARL which includes UnCover
  • Entrez
  • Institute for Scientific Information (ISI) and its Citation Reference Search (Also look at Web of science (part of Science Citation Index))
  • PubMed
• Material Safety Data Sheets (searchable)
• ModBase - Database of comparative protein structure models
• Molecular Virology at the Univ. Wisconsin
• National Center for Biotechnology Information (N.C.B.I.)
• Restriction Enzyme Database: Comprehensive Enzyme list within REBASE
• Sequence Retrival System (SRS5 at EMBL)
• Web of science (part of Science Citation Index)

• American Association for the Advancement of Science
• American Association of Immunologists
• American Cancer Society
• American Chemical Society
• American Crystallographic Association
• American Society for Biochemistry and Molecular Biology
• American Society for Cell Biology
• American Society for Microbiology
• Biochemical Society
• Biophysical Society
• British Society for Antimicrobial Chemotherapy
• Canadian Federation of Biological Societies
• European Federation of Biotechnology
• Federation of American Societies for Experimental Biology
• Federation of European Biochemical Societies
• International Union of Biochemistry and Molecular Biology
• International Union of Crystallography
• International Union of Microbiological Societies
• National Academy of Sciences
• Pittsburgh Diffraction Society
• Protein Society
• Society for Developmental Biology
• Society for Experimental Biology