and Department of Biochemistry
Molecular Modelling and Crystallographic Computing Facility
| Crystallography and Modelling: |
| Other: |
| Crystallography Links |
Crystallography and NMR Links
Compiled by Robert (rlc1@post.queensu.ca). Please let me know if you discover links that do not work.
Crystallography
Associations
- IUCr International Union of Crystallography (United Kingdom)
- CWW CrystallographyWorldWide (United Kingdom)
- ACA American Crystallographic Association
- BioSync The Structural Biology Synchrotron Users Organization -- US Synchrotron Beamlines for Macromolecular Crystallography
Databases
- The RCSB Protein Data Bank (PDB)
(Research Collaboratory for Structural Bioinformatics)
- Rutgers RCSB mirror (closer to us)
- The Worldwide Protein Data Bank
- EMBL-EBI European Bioinformatics Institute
- OCA a browser-database for structure/function
- The CCDC Home Page
- Heavy Atom Databank Database of heavy atom derivatives and structures
- HIC-Up server Hetero-compound Information Centre - Uppsala
- Backup HIC-Up server Hetero-compound Information Centre - Uppsala
- Inorganic Crystal Structure Database
- Metalloprotein Database and Browser
- Database of Macromolecular Movements Mark Gerstein, Yale U.
- The Protein Structure Database (PSdb)
- Nucleic Acid Database Project (NDB)
- Biomolecular Structure and Modelling Group, University College London
- Biocomputing group Several databases and other interesting links
- Atlas of Protein Side-Chain Interactions
- BMCD Biological macromolecule crystallization database
- HOX Database
- Structural Biology Software Database
- BIORES UK Gateway
Servers
- CRYSTOOL Computing of a high efficiency screening protocol for crystals
- Explore Symmetry On-line symmetry information like the International Tables (from the cctbx, see below)
- HIC-Up server Hetero-compound Information Centre - Uppsala
- Backup HIC-Up server Hetero-compound Information Centre - Uppsala
- CASTp server Pocket/Cavity calculations - Univ. Illinois at Chicago
- Dali server 3D structure comparisons
- EDS (Electron Density Server) server
- Matthews' Coefficient Probability Calculation Calculate the likely number of monomers in the asymmetric unit
- Yale Morph Server Mark Gerstein, Yale U.
- MolProbity Richardson's MolProbity server (requires Java)
- PRODRG Server Dundee, UK -- convert coordinates into topology files -- with ASCII sketcher
- Merohedral Crystal Twinning Server Todd Yeates and Barry Fam at UCLA Department of Chemistry and Biochemistry and UCLA-DOE Laboratory of Structural Biology and Molecular Medicine
- BMERC PSA Server Protein Structure Prediction Server
- The PredictProtein server EMBL Heidelberg
- Protein-Protein Interaction Server
Software
- CRYSTOOL Computing of a high efficiency screening protocol for crystals
- eTray Efficient Design and Recording of Crystallization Trials
- XAct 1.0 construct, maintain, and record the results of crystallisation experiments
- The ARP/wARP home page Automatic Refinement (also included with CCP4)
- bmm software MULTIDOCK, FTDOCK + several databases
- BUSTER Development Group BUSTER and SHARP: Bricogne et al.
- CHAIN Florante Quiocho's Group
- The Crystallographic Information File (CIF)
- Collaborative Computing Project Number 4 (CCP4) Home Page
- Computational Crystallography Initiative
- Computational Crystallography Toolbox
- Denzo
- HKL Research, Inc. Corporate Web Site
- Denzo under Unix
- Indexing with Denzo
- GRASP Home Page
- The Richardsons' 3D Protein Structure Laboratory and Kinemage Home Page
- Molecular Surfaces Michael Connolly
- MOOSE Macromolecular Structure Query
- The O WWW Home Page
- The PDBREPORT database
- Procheck Operating manual
- PRODRG Server Dundekk, UK -- convert coordinates into topology files -- with ASCII sketcher
- Protein Crystallography WWW Software Services Homepage
- Raster3D
- Ribbons
- Shake and Bake Hauptman-Woodward Medical Research Institute
- SgInfo Space group Info or SgInfo (Mirror site at Yale U.)
- SOLVE Automated structure solution for MIR and MAD
- SURFNET, LIGPLOT, NUCPLOT, ... Roman Laskowski
- Merohedral Crystal Twinning Server Todd Yeates and Barry Fam at UCLA Department of Chemistry and Biochemistry and UCLA-DOE Laboratory of Structural Biology and Molecular Medicine
- VMRL- Crystallographic Visualization
- X-PLOR Axel Brunger's Group
- XRayView display of diffraction geometry
- CCMS Software XtalView and others
- ZDOCK Zhiping Weng, Boston University
- CCP14: Crystallography programming resources
- CCP14: Installing Free C/Fortran Compilers
- Linux Applications in Crystallography
Methods and Experiments
- Efficient Collection of Oscillation Data (CHESS - MacCHESS)
- X-ray Anomalous Scattering (Ethan Merritt, Univ. Washington)
- MIR Phase Determination
- Recent Advances in Phasing Proceedings of the CCP4 Study Weekend, January 1997
- MAD in macromolecular crystallography J.L. Smith in Proceedings of the CCP4 Study Weekend, January 1997
- The MAD method for protein crystallography Gwyndaf Evans, Thesis
- Multiwavelength Anomalous Diffraction: Treatment of MAD Data as a Special case of MIR
Synchrotrons
- lightsources.org News, information and educational materials about the world's light source facilities
- BioSync US Synchrotron Beamlines for Macromolecular Crystallography
- World Directory of Synchrotron Instruments
- Storage ring synchrotron radiation sources around the world
- APS Advanced Photon Source
- Cornell High Energy Synchrotron Source (CHESS)
- MAX-LABORATORY Beamline BL711
- National Synchrotron Light Source (NSLS, Brookhaven)
- Macromolecular X-Ray Crystallography at the National Synchrotron Light Source
- NSLS Status Menu
- Macromolecular Diffraction at X8-C
- Macromolecular X-Ray Crystallography at X12-C
- NSLS Biology Department Web Server On BNLSTB
- Bridgeport - Port Jefferson Ferry
- New London Ct. - Orient Point, L.I. Cross Sound Ferry Services, Inc.
- Photon Factory, KEK, Japan
- SESAME Synchrotron-light for Experimental Science and Applications in the Middle East
- Stanford Synchrotron Protein Crystallography Beamlines
Personal or group pages
- Michael Wahl (CCP4 and Linux)
- Alwyn Jones, Uppsala University
- UCL Biochemistry Protein Analysis & Modelling
- Bernard Rupp's Crystallography pages
- Bart Hazes University of Alberta
- Tom Oldfield's WWW Resources for Protein Structure Analysis and Modelling
- Biomolecular Structure Center at U.Wash.
- NCBI Structure Group
- Rossmann Lab Purdue
- Yale Center for Structural Biology
- Charlie Bond some nifty perl scripts
- Ethan Merrit
- Adrian Goldman, Turku, Finland
- Wayne Hendrickson Columbia Univ./HHMI
- Zongchao Jia Queen's Univ. at Kingston
- Randy Read's group, Cambridge, UK
- Michel Sanner Scripps
Teaching (and Learning!) Crystallography
- Computer Graphics In Introductory Biochemistry
- Crystallography 101
- Crystallographic Topology
- Kevin Cowtan, Univ. York, UK Book of Fourier
- Bart Hazes' tutorials University of Alberta
- James Holton Interesting movies related to crystallography
- Optical Transforms
- XRayView Diffraction visualisation
- Teaching guide X-ray and neutron diffraction
- Teaching Crystallography
- Teaching X-ray Diffraction mirror site at Michigan State
- Merohedral Crystal Twinning Server Todd Yeates and Barry Fam at UCLA Department of Chemistry and Biochemistry and UCLA-DOE Laboratory of Structural Biology and Molecular Medicine
- Twin-Refinement with SHELXL Regine Herbst-Irmer
Commercial
Chemical suppliers
- Alfa ÆSAR Source for heavy-atom compounds
- Strem Chemicals Source for heavy-atom compounds
- Hampton Research Crystallization supplies
X-ray equipment
- ADSC Area Detector Systems Corporation
- Blake Industries e-mail address
- Bruker AXS (Formerly Siemens)
- Charles Supper Co.
- Goodfellow Suppliers of metals, polymers, ceramics & others
- HKL Research HKL, (Denzo & xdisplay)
- mar research
- Rigaku/MSC (formerly Molecular Structure Corporation (MSC)
- Nonius
- Osmic Inc. X-ray optics
- Oxford Cryosystems
- Oxford Diffraction Generators, detectors, etc.
- Oxford Instruments Another "Oxford" that makes cryo-systems
Other
NMR
Databases
- BioMagResBank
- OLDERADO NMR Ensemble Analysis Tools
Software
- ARIA Ambiguous Restraints for Iterative Assignment
- vmd-xplor NMR Visualization
- XPLOR-NIH Extensions to the original XPLOR structure determination software
- NMRView Visualization and Analysis of Nuclear Magnetic Resonance Data
- NMRPipe Spectral Processing and Analysis System
- Shifts David Case
- NMR software links
Last revised: Monday, 10-Apr-2006 17:39:32 EDT