1. NDSU Links:

2. Protein Analysis Software:

    • No links available yet.

3. Crystallography Software:

    • ARP: ARP/wARP: Crystallographic Macromolecular Model Building(Builds proteins, RNA/DNA, secondary structure, side chains, loops, solvent and ligands.)
    • CHIMERA:UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles.
    • CNS program package:The program has been designed to provide a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination.
    • COOT:Coot is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data.
    • DATA PROCESSING DPS:The Data Processing Suite (DPS) will be a complete package for processing of single crystal X-ray diffraction data of proteins, viruses, nucleic acids and other large biological complexes with emphasis on data collected at synchrotron sources.
    • Deep View Swiss-PDB Viewer:Swiss-PdbViewer (aka DeepView) is an application that provides a user friendly interface allowing to analyze several proteins at the same time.
    • DENZO-HKL:HKL Research, Inc. provides high quality software and hardware solutions for X-ray crystallography laboratories and synchrotron beam lines.
    • HEX Protein Docking:Hex is an interactive protein docking and molecular superposition program, written by Dave Ritchie. Hex understands protein and DNA structures in PDB format, and it can also read small-molecule SDF files.
    • Macromolecular Structure Database:Database that "contains crystal data and the crystallization conditions, which have been compiled from literature.
    • MADSYS:MADSYS is a software developed over the years in Wayne Hendrickson's aboratory for phasing by Multi-wavelength Anomalous Diffraction (MAD).
    • MOLMOL:Analysis and display of molecules.
    • MOLSCRIPT:MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations.
    • MOSFLM:Mosflm is 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. Mosflm can process data from a wide variety of modern area detectors, e.g. from Mar Research, Rigaku/MSC, ADSC, DIP etc.
    • POV-RAY:The Persistence of Vision Raytracer is a high-quality, totally free tool for creating stunning three-dimensional graphics.
    • PROCHECK:PROCHECK checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry.
    • Protein Explorer:Options for exploring, presenting, and sharing 3D macromolecular structure models (PDB files).
    • PYMOL:It is a user-sponsored molecular visualization system on an open-source foundation.
    • RASMOL:RasMol is a program for molecular graphics visualisation originally developed by Roger Sayle.
    • SAINT MANUAL:SAINT is a program for integrating frames, sorting refelection lists, scaling, filtering, sorting and merging of reflections.
    • SOLVE :Automated crystallographic structure solution for MIR, SAD, and MAD.
    • Structural Biology Software Database:The applications in this section are web-based tools that provides different tool for stuctural biology.
    • TNT:TNT is a program package which is used to "refine" models of macromolecules. 
    • VMD :VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
    • WHAT-IF :It is a versatile molecular modelling package that is specialized on working with proteins and the molecules in their environment like water, ligands, nucleic acids, etc.
    • XTALVIEW(CCMS):The Computational Center for Macromolecular Structure (CCMS) is distributing and supporting software for the determination and analysis of the structures of biological macromolecules.

4. Structural and Biochemical Databases:

5. Synchrotron Sources:

6. Helpful Educational Links:

7. Scientific Vendors:

Crystallography companies:

8. Other vendors:




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