CRYSTALLOGRAPHY / SAXS / STRUCTURE ANALYSIS LINKS

Structure databases

• World Wide PDB
• RCSB PDB
• PDB Europe, at EBI
• PDB Japan
• Metalloprotein database
• BMRDB (Biological Magnetic Resonance Data Bank)
• BIOISIS: Database of SAXS of Biological macromolecules

Structure solution and refinement

• Indexing and related:
  • ADXV: a program to display X-Ray diffraction images
  • DPS
  • HKL
  • Mosflm, and imosflm (the new GUI)
  • Untangle: separate overlapping diffraction patterns.
  • XDS package (xds, xscale, xdsconv)
  • XDS wiki
  • xdsme
• ARCIMBOLDO: Ab Initio protein solution far below atomic resolution.
• ARP/wARP
• Auto-Rickshaw: EMBL-HH Automated Crystal Structure Determination Platform
• BnP (The Buffalo and Pittsburgh Interface for complete protein phasing)
• CCP4
• CCP4 program documentation
• CCP4 user comunity wiki
• CNS
• Diffraction Anisotropy Server: Ellipsoidal Truncation and Anisotropic Scaling.
• Global Phasing: BUSTER-TNT and SHARP
• HIC-Up (Hetero-compound Information Centre - Uppsala)
• JLigand
• Lafire: automatic refinement
• PHENIX : Python-based Hierarchical ENvironment for Integrated Xtallography.
• phenix.refine, structure refinement.
• Computational Crystallography Newsletter.
• qFIT Server: Multiconformer modeling by constrained fitting of rotamer occupancies.
• REFMAC:
  • User's manual at the ccp4 documentation.
  • ProSMART: conformation-independent structural comparison of protein chains. Allows to generate external restraints for use in the crystallographic refinement.
• Shake and Bake
• SHARP
• Sharp Wiki
• SHELX
• Solve / Resolve
• TEXTAL : Pattern Recognition System for Interpreting Electron Density Maps.
• TLS Motion Determination
• TNT
• Molecular Replacement
  • Balbes, automatic molecular replacement pipeline.
  • CaspR, automated approach for molecular replacement.
  • EPMR and new open-EPMR
  • MrBUMP: automated Molecular Replacement.
  • NYSGRC X-ray server
  • PHASER : macromolecular crystal structures phasing with maximum likelihood methods.
  • PHASER wiki
  • Queen of Spades
• Heavy atoms:
  • HATODAS: Heavy-atom Database System
  • HEAVY-ATOM DATABANK
  • Heavy atom derivatives
  • X-ray Anomalous Scattering
  • Heavy Atom Reactivity Table
  • Heavy Atom Databases at the Shapiro Lab

Model building

• COOT
• MAIN
• O
• Alwyn Jones (A-Z of O).
• O-info , discussion list.
• Turbo-Frodo
• XtalVIEW

Structure validation

• ADIT Validation Server, at RCSB
• DDQ (Difference Density Quality), validation tool to assess the local and global correctness of macromolecular structures
• Electron Density Server (EDS) at Uppsala University.
• MolProbity
• NQ-Flipper: visualization and correction of unfavorable/incorrect Asn and Gln s/c rotamers
• PROCHECK
• SAVES: Structure Analysis and VErification Server, at UCLA.
• What If

Molecular Graphics

• BobScript
• CONSCRIPT: a programm for generating electron density isosurfaces
• Dino
• CueMol
• ENDscript
• ESPrip
• GRASP
• Jmol, a free, opensource molecular viewer written in Java.
• MolMol
• Molscript
• MolSof
• NAMOT (Nucleic Acid MOdeling Tool)
• Povscript+:
• Pov4Grasp : a patch version of POV-ray with direct support for GRASP surfaces
• Pymol
  • eMovie
  • Nuccyl
  • rTools for Pymol
  • Pymol wiki
• Rarter3D
• Spock

Structure analysis

• APBS (Adaptive Poisson-Boltzmann Solver): evaluating the electrostatic properties of biomolecules.
• Atlas of protein side-chain interactions.
• CaPTURE, cation-pi interaction analysis
• castP: A Server for Identification of Protein Pockets & Cavities
• COLORADO3D: server for the visual analysis of protein structures, includes sequence conservation coloring.
• Comparer, multiple structure aligment, outputs sequence aligment.
• ConSurf server: identification of functional regions in proteins
• DALI (3-D structure database searches) and Dali Lite (Pairwise comparison of protein structures)
• 3DNA analysis, rebuilding and visualization of nucleic acid structures.
• Dynamite: web-server that predicts protein motions.
• DynDom, Protein domain motion analysis.
• elNEMO: computes the low frequency normal modes of a protein, with potential use in difficult molrep problems.
• ESCET: analysis and comparison of 3D protein structures by T. Schneider.
• Evolutionary Trace Server
• GROMACS: molecular dynamics.
• HBexplore: analysis of hydrogen bonds in macromolecules.
• HOLE: analysis and visualisation of the pore dimensions of the holes through molecular structures of ion channels.
• Indonesia : integrated program package for biological sequence analysis. Includes Structure-based multiple sequence alignment.
• Interhlx : interhelical angles calculation.
• LigPlot : schematic diagrams of protein-ligand interactions.
• Mark-Us: A Function Annotation Server for Protein Structures.
• NACCESS Atomic Solvent Accessible Area Calculations.
• PARVATI : Protein Anisotropic Refinement Validation and Analysis
• PINTS: Patterns in Non-homologous Tertiary Structure
• PiQSi: Protein quaternary structure investigation.
• PISA: Protein Interfaces, Surfaces and Assemblies.
• PRODRG Server-Dundee
• PROPKA, empirical prediction and interpretation of protein pKa values
• ProMate, prediction of potential binding sites
• Protein Geometry Database
• Protein-Protein Interaction Server
• ProtSkin, converts a protein sequence alignment to a property file used to map the sequence conservation onto the structure.
• RAPPER server: ab initio conformational search algorithm for restraint-based protein modelling.
• SPASM server, recognition of spatial motifs( Uppsala Software Factory ).
• SSBOND: Model building of disulfide bonds (Bart Hazes)
• Structural Thermodynamics Calculations, free energy calculations from the structure of different complexes.
• STructure ANalysis server ( Uppsala Software Factory ).
• Surface Racer, calculation of accessible surface area, molecular surface area and average curvature of molecular surface, also analyses of cavities in the protein interior.
• SURFNET : Surfaces, cavities, etc.
• TOPS : protein topology cartoons (EBI)
• Uppsala Software Factory (USF).
• WebFEATURE: Automated function prediction in protein structures.
• Structural alignment :
  • 3d-SS: 3-Dimensional Structural Superposition
  • CE-MC: Multiple Protein Structure Alignment Server (Univ Albany)
  • Dali Lite (Pairwise comparison of protein structures)
  • MAPS : Multiple Alignment of Protein Structures (access via Web Server).
  • MUSTANG Multiple Strutural Alginment Algorithm (Alternative site).
  • Profit: least squares fitting.
  • RAPIDO: Rapid Alignment of Protein structures In the presence of Domain mOvements
  • StAMP: structural alignment of multiple proteins (Geoff Barton's group).
  • Stralign: Structure alignment for 3D protein structures.
  • STRAP: Multiple sequence and structure alignment.
  • TCoffee, includes Expresse 3D alignment
  • Theseus, maximum likelihood superpositioning and analysis of macromolecular structures.

Crystallization

• C6: Comparison of Crystallisation Conditions at the Collaboraty Crystallization Center
• CLIMS v2 Crystallography Laboratory Information Management System (Whisstock lab, Monash Univ)
• Crystool 4.1
• XtalGrow Software

Teaching and Tables

• Bernhard Rupp's Macromolecular Crystallography Tutorials
• Biological X-ray Structure Analysis course, by Ron Stenkamp.
• Crystallography Course: Solving an MIR structure
• EMBL Hamburg tutorial (including difracction data)
• Interactive Course of crystallography
• Kevin Cowtan's homepage
• Mike Sawaya Crystallographic Tutorials
• Bart Hazes ( Lab ) : Data collection tutorials. Find other of his tutorials here
• (IUCr) Teaching Pamphlets
• Phase Determination by Isomorphous Replacement
• X-tal protocols
• Space groups:
• Space group Hyper Tables.
• Space group Info.
• Space group Explorer (software).

Synchrotrons

• BioSync, A Structural Biologist's Guide to Synchrotron Facilities
• EUROPE
• ALBA
• DESY (Hamburg, DE):
  • EMBL Hamburg facilities.
• Diamond : Macromolecular Crystallography.
• ESRF (Grenoble):
  • Macromolecular Crystallography Group
  • ESRF User portal [SMIS]
  • ISPyB
• Swiss Light Source (SLS) at PSI:
  • DUO (Digital User Office).
  • Guest House
• Elettra (Trieste).
• Max-Lab, Lund University
• Soleil
• AMERICA
• APS (Chicago).
• NSLS (Brookhaven): Macromolecular X-ray Crystallography at the NSLS
• Stanford Macromolecular Crystallography
• ALS (Berkeley)
• Protein Crystallography Facility Group at the SRS

Suppliers: crystallization and related

• Emerald BioSystems.
• Hampton Research
• Jena Bioscience
• Molecular dimensions Ltd.
• Protein Solutions Inc.
• P212121.
• Capillary Tube Supplies Ltd
• Liquid Handling, crystallization robots and related:
• Art Robbin Instruments.
• Douglas Instruments (UK).
• Innovadyne Techonologies (UK).

X-Ray Equipment

• Bruker AXS
• Charles Supper
• Huber Diffraktionstechnik GmbH & Co. KG
• Incoatec
• Mar Research and Mar-USA
• Osmic
• Oxford Cryosystems
• Oxford Diffraction
• Rigaku

SAXS

• Svergun's Biological Small Angle Scattering Group
• BIOSIS SAXS database
• DALAI-GA, by Chacon's group
• AquaSAXS server: computing theoretical SAXS profiles with atomic models (Delarue Group)