Available upon request

RNAmmer

RNAmmer is software for predicting ribosomal RNA in full gene sequences.

To use this program at MSI, please send a a request to help@msi.umn.edu and ask to be added to the RNAmmer group. The use of RNAmmer at MSI is limited to academic researchers.

TMHMM

TMHMM is software for the prediction of transmembrane helices in proteins.

 

To use this program at MSI, please send a a request to help@msi.umn.edu and ask to be added to the TMHMM group. The use of TMHMM at MSI is limited to academic researchers.

SignalP4

SignalP4 is software for predicting the presence and location of signal peptide cleavage sites in amino acid sequences in different organisms.

 
To use this program at MSI, please send a a request to help@msi.umn.edu and ask to be added to the SignalP4 group. The use of SignalP4 at MSI is limited to academic researchers.

GeneMark-ET

GeneMark is the name of a set of gene prediction programs developed at the Georgia Institure of Technology. Genemark-ET is a member of this set of software for semi-supervised analysis of novel genomes.

To use this program at MSI, please send a a request to help@msi.umn.edu and ask to be added to the GeneMark group. The use of GeneMark at MSI is limited to academic researchers.

 

 

USEARCH

USEARCH is a unique sequence analysis tool with thousands of users world-wide. USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST.

IPA - Ingenuity Pathway Analysis

Ingenuity Pathways Analysis (IPA) is a software and database search tool for finding functions and pathways for specific biological states. It is a web-delivered application that makes use of the Ingenuity Pathways Knowledge Base, a currated database consisting of millions of individually modeled relationships between proteins, genes, complexes, cells, tissues, drugs, and diseases. It currently has data for humans, rats, and mice.

Vasp

Vasp is a package for performing ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set. The approach implemented in Vasp is based on a finite-temperature local-density approximation (with the free energy as variational quantity) and an exact evaluation of the instantaneous electronic ground state at each MD-step using efficient matrix diagonalization schemes and an efficient Pulay mixing.
 

MacVector

MacVector is a sequence analysis software for Macintosh computers. It provides sequence editing, primer design, Internet database searches, protein analysis, sequence confirmation, contig assembly capabilities, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, and a wide variety of other functions.

 

Notice to users:

Though still available for access MacVector will no longer be updated after 10/2014.   

Schrodinger, Glide, Macromodel, Jaguar, Maestro, Impact, Qsite

Schrödinger provides a complete suite of software solutions with the latest advances in pharmaceutical research and computational chemistry. These software are all available under Maestro, Schrödinger's single common graphical user interface that provides a powerful, fully-integrated molecular visualization and analysis environment. Schrödinger is widely recognized as a scientific leader in developing state-of-the-art chemical simulation software for use in pharmaceutical and biotechnology research.

CHARMM

CHARMm (Chemistry at HARvard Molecular Mechanics) is the academic version of the CHARMM simulation program available through Harvard. CHARMm uses empirical energy functions to describe the forces on atoms in molecules. These functions, plus the parameters for their functions, constitute the CHARMm force field.

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