Structural Biology

FEBio

FEBio is a nonlinear finite element solver that is specifically designed for biomechanical applications. It offers modeling scenarios, constitutive models and boundary conditions that are relevant to many research areas in biomechanics. All features can be used together seamlessly, giving the user a powerful tool for solving 3D problems in computational biomechanics.

RMBlast

"RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST+ suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program "rmblastn" for use with RepeatMasker and RepeatModeler."

UNAFold

UNAFold is a comprehensive software package for nucleic acid folding and hybridization prediction. The name is derived from "Unified Nucleic Acid Folding". Folding of single-stranded RNA or DNA, or hybridization between two single-strands, is accomplished in a variety of ways. Partition functions can be computed to derive base pair probabilities and stochastic samples of foldings or hybridizations. Energy minimization methods compute minimum free energy foldings or hybridizations, and can also compute suboptimal foldings that mimic the performance of the famous mfold software

Phenix

The PHENIX software suite is a highly automated system for macromolecular structure determination that can rapidly arrive at an initial partial model of a structure without significant human intervention, given moderate resolution and good quality data.

DSSP (DISABLED - will be removed on 12/21/17)

Note: Due to lack of use, this software module has been disabled and will be removed from MSI systems on 12/21/17. If you need this software, please contact help@msi.umn.edu.

 

The DSSP program was designed by Wolfgang Kabsch and Chris Sander to standardize secondary structure assignment. DSSP is a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB). DSSP is also the program that calculates DSSP entries from PDB entries.

GROMACS

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

Discovery Studio

Discovery Studio® provides the most advanced software solutions for life science researchers available today. From project conception to lead optimization, Discovery Studio includes a diverse collection of sophisticated software applications to take your research to the next level, all conveniently packaged into a single, easy-to-use Linux- or Windows-based environment.

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