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Crystallization |
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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 |
This website contains entries for refolding protocols for a wide range of proteins. | This server provides information about proteins that lack fixed 3D structure in their putatively native states. |
Crystallography |
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Data processing |
The triad of Denzo, XDisplayF and Scalepack: programs to visualize and interpret X-ray diffraction images. | DPS/Mosflm | 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 |
Software suite for the automated determination of macromolecular structures using X-ray crystallography and other methods.(i.e. phenix.xtriage,phenix.refine) | 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 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 |
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 |
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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). | |
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 |
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 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. | |
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 |
Databases |
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Crystallographic society |
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ACA (American Crystallographic Association) |
IUCr (International Union of Crystallography) |
Biophysics Society of R.O.C | NSRRC Bio-Server |