Collaborative Computational Project Number 14
for Single Crystal and Powder Diffraction
CCP14
Some Starting links to Protein Crystallography Software/Macromolecular Crystallographic Software
The CCP14 Homepage is at http://www.ccp14.ac.uk
- List of Software via UAB Center for Macromolecular Crystallography -
http://www.cmc.uab.edu/
- List of Software via UAB Center for Macromolecular Crystallography -
http://ppcii.scripps.edu/links.html
- List of Software via "Practical Protein Crystallography" homepage -
http://imsb.au.dk/~mok/o/
- MAIN (is an interactivelly driven computer program dealing with computational parts of macromolecular crystallography) : -
http://www-bmb.ijs.si/doc/index.html.
(Thanks to Lalji for this link)
- Classification of Software for Macromolecular Crystallographers: -
http://www-bmb.ijs.si/doc/other_index.html.
- List of Software via PDB homepage -
http://www.rcsb.org/pdb/software-list.html
- Macromolecular Crystallography Program Documentation at CSB Yale University -
- Macromolecular Crystallography Program Documentation at University of Massachusetts Medical School -
http://bragg.ummed.edu/programs3a.html
- DENZO Data Processing -
http://www.hkl-xray.com
- DPS/MacCHESS Data Processing -
http://www.chess.cornell.edu/MacCHESS/processing_gui.html
- PHASES Suite -
http://www.imsb.au.dk/~mok/phases/phases.html
- CCP4 Suite -
http://www.dl.ac.uk/CCP/CCP4/main.html
- SHELX refinement and structure solving program -
http://shelx.uni-ac.gwdg.de/SHELX/index.html
- TNT Macromolecular Refinement Package -
http://www.uoxray.uoregon.edu/tnt/welcome.html
- MAIN - interactivelly driven computer program dealing with computational parts of macromolecular crystallography -
http://www-bmb.ijs.si/doc/
- MICE - Molecular Sciences and Interaction Environments -
http://mice.sdsc.edu/
- CNS - Crystallography and NMR System -
http://xplor.csb.yale.edu/cns_solve/
- PROTEIN - A program system for the crystal structure analysis of macromolecules -
http://www.biochem.mpg.de/PROTEIN/
- SOLVE - Automated crystallographic structure solution for MIR and MAD -
http://www.solve.lanl.gov/
- Watncs - Pick water molecules which follow NCSs and sort out them to NCS asymmetric unit -
http://gamma.mbb.ki.se/~guoguang/watncs.html
- Conscript (A program for generating electron density isosurfaces
for presentation in protein crystallography) -
http://www.bioresi.com.au/conscript/
- whatif - "WHAT IF is a versatile protein structure analysis program
that can be used for mutant prediction, structure verification, molecular graphics" -
http://www.sander.embl-heidelberg.de/whatif/
- SnB - Shake-and-Bake - Structure Solution -
http://www.hwi.buffalo.edu/SnB/
- LIGPLOT - Program for automatically plotting protein-ligand interactions -
http://www.biochem.ucl.ac.uk/bsm/ligplot/ligplot.html
- HBPLUS - program for calculating hydrogen bonds and hydrophobic contacts for plotting by LIGPLOT -
http://www.biochem.ucl.ac.uk/~mcdonald/hbplus/home.html
- Procheck - A program that checks the stereochemical quality of a protein structure -
http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html
- Profit - A program for fitting protein structures on to each other -
http://www.biochem.ucl.ac.uk/~martin/programs/index.html#profit
- PROCOMP - Compares residue-by-residue geometry of a set of closely-related protein structures. -
http://www.biochem.ucl.ac.uk/~roman/procheck_comp/procheck_comp.html
- NACCESS - program for computing solvent accessible areas -
http://sjh.bi.umist.ac.uk/naccess.html
- AMBER - Assisted Model Building with Energy Refinement -
http://www.amber.ucsf.edu/amber/amber.html
- ARP and WARP Phasing Software -
http://www.embl-hamburg.de/ARP
- Cai X.-J. Zhang's Molecular Replacement Package -
http://omrf.uokhsc.edu/~zhangc/mrx/mrx.html
- Michael S. Chapman's Real Space Refinement Package -
http://www.sb.fsu.edu/~rsref/
- Buster - (A program for recovering missing phase information by Bayesian inference) -
http://lagrange.mrc-lmb.cam.ac.uk/
- SHARP (A Statistical Heavy Atom Refinement and Phasing program) -
http://lagrange.mrc-lmb.cam.ac.uk/sharp/SharpHome.phtml
- The Biochemist's ToolBox (links to databases, etc) -
http://www.biochem.ualberta.ca/Biochem/BioLinks.html
- 3D Reconstruction (Cryo-electron microscopy (Virus reconstruction), etc)-
http://biocomp.stanford.edu/3dreconstruction/index.html
- EMBL Virus Structures Image Database -
http://www.embl-heidelberg.de/ExternalInfo/fuller/icos0.html
- EMBL Virus Structures Image Database -
http://www.bocklabs.wisc.edu/virusviztop.html
- Image Library of Biologial Macromolecules Image Database -
http://www.imb-jena.de/IMAGE.html
- Molecules-R-Us (NIH) Image Database -
http://molbio.info.nih.gov/doc/mrus/mol_r_us.html
- SWISS-3DIMAGE Annotated 3-D Image Database -
http://www.expasy.ch/sw3d/sw3d-top.html
- An Internet course on The Principles of Protein Structure -
http://www.cryst.bbk.ac.uk/PPS/index.html
- SWISS-MODEL - An Automated Comparative Protein Modelling Server -
http://www.expasy.ch/swissmod/SWISS-MODEL.html
- Glaxo Wellcome Experimental Research presents the Swiss-PdbViewer Software for Mac PC SGI and Linux -
http://www.expasy.ch/spdbv/mainpage.htm
- PovRay (Persistance of Vision Raytracing software) -
http://www.povray.org
- X-plor (Yale) - http://xplor.csb.yale.edu/xplor-info/
- Molecular Structure Determination Packages Supported at Pittsburgh Supercomputing Center (PSC), Carnegie Mellon University -
http://www.psc.edu/general/software/categories/molecular_structure_determination.html
- X-plor (MSI) -
http://www.msi.com/about/offers/xplor/index.html
- Xsight (MSI) suite -
http://www.msi.com/solutions/products/insight/modules/xsight.html
- XtalView Refinement, fitting and graphics (Structure and Contour Map) -
http://www.sdsc.edu/CCMS/Packages/XTALVIEW/xtalview.html and
http://www.scripps.edu/pub/dem-web/
- TURBO_FRODO Web site -
http://afmb.cnrs-mrs.fr/TURBO_FRODO/turbo.html
- TURBO_FRODO Description with on-line manual -
http://www.med.yale.edu/computing/acadcomp/research/turbo/turbo_descrip.html
- MAPS (an automated program for Multiple Alignment of Protein Structures) -
http://gamma.mbb.ki.se/~guoguang/maps.html |
http://bioinfo1.mbfys.lu.se/TOP/maps.html
- List of available programs from Guoguang Lu -
http://bioinfo1.mbfys.lu.se/~guoguang/prog.html
- DIFLIST Checking the atoms with negative value in Fo-Fc map
- DOMID Identify protein domains from 3d structures
- FINDNCS find out NCS operations from heavy atom sites
- FIT A structure comparison utility program
- FOCUS A program which draw the atoms, bonds and their density maps
- MAPS An automated program for Multiple Alignment of Protein Structures
- MATROT An utility program for rotation functions
- PATTERN A precession simulation program (figure)
- PSHIF Detect domain movement
- PERCENT calculate percentage of completness
- PDBSYMOP give symmetric operations to PDB
- REINDEX reindex the ascii hkl reflxn file by a transform matrix
- ROTCENTR rotate and translate molecule
- TOP An automatic structure comparison program (Web server)
- WATNCS Pick waters which follow NCSs and sort out to NCS assymetric unit
- FRODO/TOM Molecular Modelling Program -
http://www.iucr.org/sincris-top/logiciel/prg-frodo.html
- Online Documentation for Macromolecular software (Frodo, etc, etc, etc) -
http://www.imb-jena.de/www_sbx/sbx_dhp_od.html
- "O" (includes links to other software) Graphics -
http://imsb.au.dk/~mok/o/
- MolScript v. 2.0 Graphics (MolScript: The Official Web Site) -
http://www.avatar.se/molscript/
- Spock is a full-featured molecular graphics program,
knows about crystallographic symmetry (and also allows shared screens/conferencing over the internet):
http://quorum.tamu.edu/spock/
- RasMol and Chime Graphics -
http://www.umass.edu/microbio/rasmol/
- Herbert Bernsteins version of RasMol Graphics -
http://www.bernstein-plus-sons.com/software/rasmol/doc/rasmol.html
- Raster3D Graphics -
http://www.bmsc.washington.edu/raster3d/
- The DNA modelling course HomePage
- Web cutter.
- PovChem
- "PovChem takes molecules in the PDB format, lets you to set up a picture with
fine control over details of the illustration - colors, atom and bond radii, view
orientation, etc. It will even calculate and display hydrogen bonds."
- http://www.ChemicalGraphics.com/PovChem/
- DNA (organics and proteins) Graphics Created with PovChem for Windows, Mac and UNIX
- Ribbons Software Home Page (Molecular Graphics)
- Other molecular graphics sites
- MOLMOL - MOLecule analysis and MOLecule display
- PREPI
- "PREPI is a molecular graphics program which can be used to EASILY
produce and interactively manipulate many different types of molecular
representations (cartoons) as well as providing quantative information
on secondary structural topology. The program is not just limited to
proteins, but can also show cartoon representations of NUCLEIC ACIDS."
- http://www.bmm.icnet.uk/people/suhail/prepi.html
- WHAT IF
- "WHAT IF is a versatile protein structure analysis program that can be
used for mutant prediction, structure verification, molecular graphics, etc."
- http://www.cmbi.kun.nl/whatif/
- 3D modeling homepage
- 3D modeling services
- BIOcomputing 3D modelling unit servers
- "PredictProtein.
Multiple alignments; predictions of secondary structure, accessibility, and helical transmembrane regions; (threading); evaluation of
prediction accuracy.
K2D Protein secondary structure prediction from CD spectra.
PROPSEARCH Compositional search of sequence databases using a sequence or experimental amino acid analysis data.
MAXSPROUT (Re)constructing full coordinates from C-alpha atoms.
DALI. Comparison of protein structures in 3D
Protein Structure Verification 'BIOTECH' Protein Structure Verification server.
Small molecule topology maker The PRODRG server takes a small molecule and produces WHATIF and GROMOS topology files."
- http://swift.embl-heidelberg.de/servers/
- The EMBL-Heidelberg Amino Acid Analysis Server
- 3D modelling services
- "DSSP: Definition of Secondary Structure of Proteins
FSSP: Families of Structurally Similar Proteins
HSSP: Homology-derived Secondary Structure of Proteins
PDBSELECT: Unique subset of 3-D protein structures
PDBFINDER: Your entry into the PDB database
PDBREPORT: Structure verification reports for PDB structures
GPCRDB: G protein-coupled receptor (GPCR) data
Modules in extracellular proteins"
- http://swift.embl-heidelberg.de/future/databases.html
- DNA Sequence & Structural Analyses
- (almost every link imaginable relating to DNA sequence analysis plus DNA to protein sequencing)
- "DNA Sequence Homology Analysis and Searching
DNA/RNA Structure & Function Analyses
Multifunction Search & Data Retrieval Searchers
Nucleotide Sequence Alignment Servers
Sequence Manipulation Tools
Miscellaneous Analyses "
- http://www.unl.edu/stc-95/ResTools/biotools/biotools16.html