1. NDSU Links:
2. Protein Analysis Software:
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:
- Antibiotics - sequence and structure :
- Cambridge Structure Database (CCDC): The CCDC is dedicated to the advancement of chemistry and crystallography for the public benefit through providing high-quality information services and software.
- DALI (protein structure comparison):The Dali server is a network service for comparing protein structures in 3D.
- Database of Interacting Proteins (DIP):The DIPTM database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions.
- EC Enzyme Database:This Web version of EC Enzyme has hot links among its own entries and to the following Databases:
- OMIM - Online Mendelain Inheritance in Man
- SWISSPROT - The Swiss Protein Database
- EMBL-EBL:The European Bioinformatics Institute (EBI) is an academic research institute located on the Wellcome Trust Genome Campus in Hinxton near Cambridge (UK), part of the European Molecular Biology Laboratory(EMBL).
- European Bioinformatics Institute (EBI):The EBI provides access to many tools for browsing and retrieving biological related sequence and literature data.
- Heavy-Atom Databank:databank contains information resulting from an analysis of the binding of these heavy-atoms with proteins in the crystal environment.
- Intein database server (at NEB):InBase is a curated database devoted to inteins.
- ModBase - Database of comparative protein structure models:
- Molecular Modeling Database (MMDB) - Entrez Structure:The Molecular Modeling Database (MMDB), as part of the Entrezsystem, facilitates access to structure data by connecting them with associated literature, protein and nucleic acid sequences,chemicals,biomolecular interactions,and more.
- Nucleic Acid Database:a repository of three-dimensional structural information about nucleic acids.
- PDB: The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies.
- RCSB PDB Software Tools:An Information Portal to Biological Macromolecular Structures.
5. Synchrotron Sources:
6. Helpful Educational Links:
7. Scientific Vendors:
Crystallography companies:
8. Other vendors:
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