A Selection of Software used in Biological Crystallography

Integrated Package Data Collection - Processing Phasing and Refinement Molecular (Re)Placement Model Building Graphics Structure Validation Structure Similarities

Crystallographic computing Sequences Analyses  Analyses of proteins (3D to functions) Databases Domains Predictions. Order/Disorder Fold Predictions and homology building Automated Structure determination

Tutorials and Courses Structural Genomics Miscellaneous Links Bibliography

 

• DBGS/CEBGS specific  informations

• Short informations on local installation of programs

• My selection of articles for students

• My selection of articles for students (old file)
  

• Selection of programs
  

IntegratedPackage

• CCP4
  • "CCP4 Roadmaps"
  • CCP4 Tutorials
  • CCP4 wiki
• PHENIX
• XtalView
• CNS

 

Data Collection and Processing

• HKL2000
  • HKL2000 Documentation (pdf)   © HKL2000
  • HKL2000 Manual (HTML)

• autoPROC
  
  • autoPROC wiki

• MOSFLM( integrated in CCP4), new Mosflm GUI : imosflm
  • Mosflm and Scala: A Quick Tutorial Crystallography (SSRL)
    
  • MOSFLM Help and Guidance
  • MOSFLM User Guide
  • imosflm
• XDS
  • xdswiki
    
• d*TREK (CEBGS, © RIGAKU PDF documents)
  • d*TREK, "overview"
  • d*TREK, "Getting Started"
  • d*TREK, " Complete Manual"(674 pages !)

• Data reduction: Pointless, Aimless, Truncate (integrated in CCP4, ccp4i)
• See PHENIX  for Xray data analyses, twinning analyses and other tools.
  • Assessing data quality with phenix.xtriage
  • Space group and others problems.  try Zanuda from YSBL server
• see also XPREP from SHELX

Phasingand Refinement

• ARP_wARP(integrated in CCP4)
• BUSTER, autoBuster
  
  • "Buster Wiki"
• CRANK
• CNS
• PHASES
• PHASER
• PHENIX
  • Home Site
  • Documentation.
  • Phenix CCP4 Wiki
• REFMAC
• SHARP
  • "Sharp manual"
• SHELX.
  • GraphicInterface to SHELX :HKL2MAP
  • a tutorial
    
• SnB
• Solve  (included in PHENIX. Use phenix.autosol)

• TLS server

Molecular(Re)Placement

• Automated Process

MrBUMP        BALBES         CaspR   

• Programs

Model Building

• O (Home page of Alwyn Jones)
  • O12
  • Local informations
• Coot
  • Manuel
  • tutorial
• MIFit

• Getting  ligand coordinates and generating  dictionnaries
  • Ligands in PDB
  • Ligand-depot
  • HIC-Up
  • Dundee prodrg server 
  • EBI MSD-CHEM server
  • Procognate
  • bioinformatic tools and databases for glycobiology
• Building a new ligand and generating  dictionnaries
  • elbow (from PHENIX package)
  • QDS in O12
  • Sketcher(integrated in CCP4)
  • JLigand
    
• Nucleic Acid structures
  • Web 3DNA for analysis, reconstruction and visualization of nucleic-acid structures
  
  

Structure Validation

	MolProbity	JCSG   SAVES	Verify3D	SFCHECK	VADAR	What IF
	STAN

   

• Auto-Rickshaw Seb Server, EMBL Hamburg.
• See Also Elves
• See Also CCP4 Server to run :Balbes, MrBUMP, Zanuda, AMPLE, SHELX, CRANK2

 3D Analyses. From 3D to Function

• ProFunc
• ProKnow
• I-Tasser
  

• CASTp  Server: Pockets and Cavities
• GRASP

• PISA
• Pita
• SPIDDER

• TLS Motion 
• elNemo (NMA)
• Escet

 

Graphics

PyMol

RIBBONS

Setor

NOC

CueMol

DINO

MolScript

Molray

Nucplot

Rasmol

Namot

Raster3D

VMD

TOPS (Protein Topology)

Swiss - PDB Viewer

Structure Similarities

DALI

MATRAS

PAPIA

TOPS (3D)

VAST

 

Databases

• CATH
• Heavy Atom Databank (Imperial College)
• Heavy Atom Databank (HATODAS, RIKEN)
• PDB-RCSB
  • wwPDB
    • wwPDB Remediation Project
  • PDB Format   (HTML)  (PDF)
    
  • IUPAC recommendations
  • OCA Browser
  • MSD
  • PDBSUM
  • SRS3D
• PDBe
  

• SCOP

DomainsPredictions. Order/Disorder

	Globprot	IUPred	DisEMBL	PONDR	drawhca	disprot
	FoldIndex
	CDD	Scooby

Crystallization tools

• XtalPred. Prediction of  protein crystallizability
• Surface Entropy Reduction prediction (SERp)

 

Fold Predictions and building by homolgy

• Fold Recognition FFAS
• Fold Recognition PHYRE(successor of  3D-PSSM)
• I-Tasser
• PHD
• PROSPECT
• 123D
• MC-FOLD
  

 

Building by homology

• SCWRL Server
• Modeller
• Links to Structural bioinformatics databases and softwares

 

Miscellaneous

• Crystallographic Space Group Diagrams and Tables
• Matthews Coefficients
• Computational Crystallography Toolbox
• International Tables Of Crystallography (Vol I)
• Space group decoder
• Uppsala Software Factory

• The Protein Structure Initiative Structural Genomics Knowledgebase
• JCSG
• MCSG
• Open Protein Structure Annotation Network (TOPSAN)

 

Links

• Crystal-Links
• Structural Biology (Drunback)
• Twinning Center
• PubMed

SequencesAnalyses

Mafft

Tcoffee

ClustalX

ProbCons

Pipe_Align

BT MPIDB

pfaat

BioEdit

Chimera

TexShade

EMBOSS

BIPS

 
Bibliography

• my selection of articles for students (Master degree, in French)

• Free Bibliographic tools (“Endnote-like”)
  • Zotero (FireFox extension)     Bibus
  • JabRef

 

 Courses

• Protein Crystallography Course (Cambridge, UK)
• MAD Phasing 1
• X-ray Anomalous Scattering

• BESSY
• EMBL
• xdswiki
• AUTOSTRUCT-TEST DATA

CrystallographicComputing

• IUCR commission 2005, Speakers' Notes and Tutorial Notes
• Computational Crystallography Toolbox
• Maths
  • C.a.R
  • Maxima