learning crystallography | crystallization | data processing & scaling | heavy atom search | phasing & refinement | modeling & graphics | molecular replacement | picture drawing | structure evaluation | structure analyses | synchrotron | others

learning crystallography

Introduction of protein crystallography
Multiple wavelength Anomalous Diffraction(MAD)
Theory and methods of data analysis
Space groups
Anomalous dispersion
Reciprocal cell calculation
Protein crystallography on the web


Pictorial library
Hampton research
Emerald biostructure
Crystallization database
Guide to crystallization
Practical guide of crystallization

data processing & scaling

HKL Package
Strategy of processing
Example of Mosflm and SCALA
Autoindexing with DENZO
HKL manual

heavy atom search

Heavy atom databank
Heavy atom library
About Xenon
Procedure of derivative

phasing & refinement

ARP/wARP A system for the refinement of protein structures via automatic updating and re-building of the model and solvent structure
CCP4 A suite of programs covering all aspects of crystallographic structure determination, refinement and analysis
CHART Automatic Structure Solution
CNS A system for structure determination from crystallographic or NMR data
PHASES Compute phase angles for diffraction data from macromolecular crystals
SAPI heavy atom search program using direct methods
SHELX A set of programs for direct structure solution and refinement with high resolution diffraction data
SNB dual-space direct-methods procedure for determining crystal structures from X-ray diffraction data
SOLVE An automated system for phase determination from MIR and MAD data
XtalView An interactive system for building and manipulating models in electron density map and for phase determination from MIR or MAD data.
USF software O related softwares in Uppsala Software Factory

modeling & graphics

ARP/wARP An automatic model building program
An interactively driven suite of programs for molecular modeling, density modification, model refinement and structure analysis
An interactive system for building and manipulating models in electron density maps
XtalView An interactive system for building and manipulating models.
HiCUP Ligand database
prodrg .pro .top file generation
corina Ligand drawing

molecular replacement

MR tutorial from data to density
Amore in CCP4
Queen of Spade

picture drawing

Alscript sequence alignment and drawing
BioEditor A tool for creating and viewing dynamic, formatted structure annotations; for Windows
DINO 3D visualization program for structural biology data
ProteinScope Free viewer to display and manipulate PDB files and create animations and slides of proteins
Raster 3D
Ribbons A program for molecular illustration and error analysis
VMD Visual Molecular Dynamics
MSMS a molecular surface computation
MEAD Macroscopic Electrostatics with Atomic Detail

structure evaluation

Biotech Validation Suite
ERRAT Structure Submission Page
Verify3D Structure Evaluation Server

structure analyses

ASC The Analytic Surface Calculation Package
The ASTRAL compendium Databases and tools useful for analyzing protein structures and their sequences
CAST A Server for Identification of Protein Pockets & Cavities
CastP Server that calculates measurements of structural pockets and cavities of proteins and nucleic acids
CATH Class, architecture, topology and homologous superfamily
CE/CL Alignment server and databases for structure comparison by Combinatorial Extension (CE) and Compound Likeness (CL)
CAMPASS CAMbridge database of Protein Alignments organized as Structural Superfamilies
ConSurf Server for the Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information
Culled PDBM Representative PDB structures
DALI Comparison of protein structures in 3D
DSMP Database of Structural Motifs in Proteins
eF-site Electrostatic-surface of Functional site
Grass Graphical Representation and Analysis of Structure Server
HIC-Up Hetero-compound Information
HOMSTRAD Homologous Structure Alignment Database
IMB Jena Image Library of Biological Macromolecules Provides information on sites included in three-dimensional biopolymer structures
IMB Jena Image Library Site Database Provides information on sites included in three-dimensional biopolymer structures
Library of Protein Family Cores
Ligand-Protein Contacts and Contacts of Structural Units A resource which provides an analysis of interatomic contacts in ligand-protein complexes (LPC) or an analysis of interatomic contacts in protein entries (CSU)
Macromolecular Structures Database
Morphology of Protein-Protein Interfaces A visual survey of protein-protein interfaces in homodimeric proteins from the PDB
NRL 3D Sequence-Structure Database produced by PIR
OLDERADO On Line Database of Ensemble Representative And DOmains
PALI Phylogeny and ALIgnment of homologous protein structures
PartsList Dynamic protein fold ranking by disparate attributes, including whole-genome expression and interaction information
PDB select Representative PDB structures
PDBSum Summaries and structural analyses of PDB data files
PQS EBI MSD Protein Quaternary Structure database
SCOP Structural Classification of Proteins (UK), mirrored around the world
SCOR Structural Classification Of RNA
Protein Sidechain Webpage Information on sidechain conformational analysis, sidechain rotamer libraries, and sidechain conformation prediction
STING Sequence To and withIN Graphics (USA), mirrored in Israel
SPIN-PP Surface Properties of Interfaces - Protein Protein interfaces
TOPS-Protein Topology


Structural biology synchrotron users organization biosync
ALS - Advanced Light Source
CAMD/LSU Synchrotron
DESY, EMBL- Hamburg
ESRF, EMBL- Grenoble
Gulf Coast Protein Crystallography Consortium
Photon Factory (Protein Crystallography)
Pohang accelerator laboratory
Beamline 6B of pohang accelerator laboratory