Useful link


 Protein Crystallography Teaching Links 
Protein Crystallography Universe A general protein crystallography portal containing information about software, websites, jobs, journals, organizations, education, etc. Crystallography 101 An introductory crystallography course by Bernhard Rupp
Research tools for the crystallization of proteins, peptides, nucleic acids, and small molecules. CCP4-basic maths for Protein Crystallographers Maths for potein crystallographers, see also list of alternate origins for centrosymetric space groups and non-centrosymetric space groups.

 Protein stability 
Refold This website contains entries for refolding protocols for a wide range of proteins. DisProt
This server provides information about proteins that lack fixed 3D structure in their putatively native states.


 Data processing
HKL2000 The triad of Denzo, XDisplayF and Scalepack: programs to visualize and interpret X-ray diffraction images. A program for integrating single crystal diffraction data from area detectors. It is assumed that the experiment was conducted using the Arndt-Wonacott oscillation method, and also that monochromatic radiation was used.

 Structure dtermination
Phenix Software suite for the automated determination of macromolecular structures using X-ray crystallography and other methods.(i.e. phenix.xtriage,phenix.refine) CNS Crystallography & NMR System (CNS) has been designed to provide heavy atom searching, experimental phasing (including MAD and MIR), density modification, crystallographic refinement with maximum likelihood targets.
The CCP4 program suite is a collection of disparate programs covering most of the computations required for macromolecular crystallography. For more information, see ccp4 wiki and ccp4bb. SHARP/autoSHARP A computer program for refining a model of isomorphous heavy-atom substitution and calculating phase probabilities from it.( MIR(AS), SIR(AS), SAD or MAD)
XtalView32 A complete package for solving a macromolecular crystal structure by isomorphous replacement, see user manual. The Dundee PRODRG2 Server Convert coordinates for small molecules in PDB format to the following topology formats: GROMOS, GROMACS, WHAT IF, CNS, O, SHELX, HEX and MOL2.
 Molecular modeling environment
Coot Coot displays maps and models and allows model manipulations such as idealization, real space refinement, manual rotation/translation,rigid-body fitting,..etc. For more information, see coot wiki and coot user manual . O The program is aimed at scientists with a need to model, build and display macromolecules.
TURBO FRODO Reads and displays X-ray density maps. See user manual.

 Molecular graphics package
pymol A free and flexible molecular graphics and modelling package which can be also used to generate animated sequences. For detail information, see pymol wiki and pymol user manual. Molscript  MolScript is a program for creating schematic or detailed molecular graphics images from molecular 3D coordinates. 

Protein Sequence and Structure Analysis
 2nd Structure Prediction 
PSIPRED PSIPRED is a simple and reliable secondary structure prediction method, incorporating two feed-forward neural networks which perform an analysis on output obtained from PSI-BLAST (Position Specific Iterated - BLAST). HYPROSPII A knowledge-based hybrid method for protein secondary structure prediction based on local prediction confidence.

 Motif & 3D Domain Search
This page provides the overview of the Motif search service on GenomeNet. pFam
(Protein Family Database)
The Pfam database is a large collection of protein families, each represented by multiple sequence alignments  and hidden Markov models (HMMs).
Smart Simple modular architecture research tool

 3D Structure Comparison
CE-Combinatorial Extension Method  Databases and tools for 3-D protein structure comparison and alignment. Dali The Dali server is a network service for comparing protein structures in 3D. 
VAST- NCBI Structure-structure similarity search service.

 3D Structure Threading
Phyre Web-based Method for Protein Fold Recognition using 1D and 3D Sequence Profiles coupled with Secondary Structure and Solvation Potential Information. It's a new vision of 3Dpssm.
PS2 is an automated homology modeling server. Made in Taiwan! 
I-tasser I-TASSER is an Internet service for protein structure and function predictions. Super powerful !! NCBI-threading Protein sequence-structure threading

 Protein-Protein or Protein-DNA interactions
PROTORP is a tool to analyse the properties of interfaces in the 3D structures of protein-protein associations. Protein-Nucleic acid interaction server Analyse the protein interface of protein-nucleic acid complex. You can submit the coordinates of a complex of your choice and then view tables describing the nature of the interface.
PISA PDBePISA is an interactive tool for the exploration of macromolecular (protein, DNA/RNA and ligand) interfaces, prediction of probable quaternary structures (assemblies), database searches of structurally similar interfaces and assemblies, as well as searches on various assembly and PDB entry parameters. Protein-DNA Interface Database Collection of various natural and engineered zinc finger proteins, containing sequence features and linked to their structures.

 Other Links for Bioinformatics
UCLA-DOE Softberry Molecular Biology Database List  IMB Bioinformatics Core Paul's Science Links 


(Protein Structure Classification)
(Protein Structure Classification) 
molecular biology 
(National Center for Biotechnology Information,USA) 
pFam Server
(Protein Family Database)
Protein Data Bank  Nucleic Acid Database  EBI (European Bioinformatics Institute)
(Fold classification based on Struture-Structure alignment of Proteins) 
IMB Jena Image Library of Biological Macromolecules (containing metal-binding proteins)  Hetero-Compound Crystallographic Server 

Crystallographic society

(American Crystallographic Association)

(International Union of Crystallography)
Biophysics Society of R.O.C NSRRC Bio-Server