> Structural Biology1,2
Amber
A program for molecular simulation using mechanical force fields that were developed for proteins and nucleic acids. (cluster)
CCP4
A collection of programs for solving protein, DNA, and RNA structures from X-ray diffraction data. These include programs for scaling, indexing, and phasing reflection data, and for refining structure models.
CNS
A data analysis environment for solving protein, DNA, and RNA structures using either X-ray diffraction data or NMR data. CNS evolved from Xplor and is developed by the same authors. (cluster)
DYANA
A program for calculating protein structures from NMR experimental data, including NOE distance restraints and torsion angle restraints. DYANA is no longer supported by its authors, but its functionality has been included in its successor program, CYANA, (hc-alpha)
Cyana
A program for calculating protein structures from NMR experimental data; see the DYANA description.
Sharp
A program for phasing X-ray crystallography data. The data must first be indexed, merged, and scaled using other programs (such as CCP4).
SnB
A program for solving crystal structures of small molecules (not proteins) using direct methods (solving many simultaneous equations). It can be used for molecules of up to 1000 non-hydrogen atoms.
Felix
A program for phasing, viewing, and assigning peaks in 1D and 2D NMR data. Modules can be added for computer-assisted peak assignment and processing additional dimensions.
Tripos
Tripos makes several programs for molecular modeling and visualization. The base product, SYBYL, can build, view, and optimize molecular structures, allowing a choice of force fields to be used for optimization.
Xplor
A program for solving protein, DNA, and RNA structures using either X-ray diffraction data or NMR data. It explores the conformational space available to macromolecules based on restrictions imposed by experimental data and empirical energy functions.(cluster)
Modeller
A program for comparative modeling of protein structures. Modeller can calculate a structure from a protein sequence if it is aligned to another protein sequence whose structure is known. It can also be used to optimize a structure based on energy minimization. (hc-alpha, cluster)
Denzo
A program for automatically determining the lattice type, space group, and unit cell dimensions of crystals from X-ray diffraction data.
HKL2000
The HKL2000 package is a collection of programs for processing each oscillation image in an X-ray crystallography experiment. It includes Denzo for indexing the crystal, Scalepack for scaling reflection intensities (to account for radiation damage), and XDisp for displaying images.
1Please contact your Local Support Provider (LSPs) to have any of these applications installed on your system. Click on the link below for a complete listing of the LSPs and their contact information: http://www.hartwellcenter.org/bio_rescom/clientSer/contactlsp.php
2To establish an account on a computer system, please fill out the Account Request Form and return to Bioinformatics (room D1010, first floor DTRT).