TSN 1.0 – Expression Classification method from Small numbers of Biomolecules

TSN 1.0

:: DESCRIPTION

TSN (Top-scoring ‘N’ algorithm) uses a flexible classifier size to expand the permutation and combination space available for classification.  TSN relies on an unusual number system known as factoradics to easily translate between permutations of features and decimal numbers.

::DEVELOPER

The Hood-Price Lab for Systems Biomedicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • Matlab

:: DOWNLOAD

  TSN

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Sep 11;13:227. doi: 10.1186/1471-2105-13-227.
The top-scoring ‘N’ algorithm: a generalized relative expression classification method from small numbers of biomolecules.
Magis AT, Price ND.

SMOG 2.2 – Structure-based Models for Biomolecules

SMOG 2.2

:: DESCRIPTION

SMOG is a versatile software package for generating structure-based models.SMOG 2 is a downloadable software package that reads user-designated structural information and user-defined energy definitions, in order to produce the files necessary to use SBMs with high performance molecular dynamics packages: GROMACS and NAMD.

::DEVELOPER

SMOG team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SMOG

:: MORE INFORMATION

Citation

SMOG 2: A Versatile Software Package for Generating Structure-Based Models.
Noel JK, Levi M, Raghunathan M, Lammert H, Hayes RL, Onuchic JN, Whitford PC.
PLoS Comput Biol. 2016 Mar 10;12(3):e1004794. doi: 10.1371/journal.pcbi.1004794

PathBinder 1.0 – Explore Literature, Annotate Metabolic and Regulatory Interactions and Biomolecules

PathBinder 1.0

:: DESCRIPTION

PathBinder is a unique, plant-based tool to explore literature, and to annotate metabolic and regulatory interactions and biomolecules. PathBinder queries the MEDLINE database and retrieves sentences containing two terms of interest, and rank them based on their probability to describe interactions between the two given terms; each sentence is a clickable link pointing to the original online PubMed citation.

::DEVELOPER

Lifeng Zhang zlfpeak@iastate.edu

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 PathBinder

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S18.
PathBinder–text empirics and automatic extraction of biomolecular interactions.
Zhang L, Berleant D, Ding J, Cao T, Syrkin Wurtele E.

GeoStaS 1.2 – Divides a biomolecule into Dynamic Domains

GeoStaS 1.2

:: DESCRIPTION

GeoStaS divides a biomolecule (proteins, nucleic acids and their complexes) into dynamic domains based on its different conformations, obtained from experiments or simulations.

::DEVELOPER

Biomolecular Machines Laboratory 

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GeoStaS

:: MORE INFORMATION

Citation

Julia Romanowska Krzysztof S. Nowiński and Joanna Trylska
Determining Geometrically Stable Domains in Molecular Conformation Sets
J. Chem. Theory Comput., 2012, 8 (8), pp 2588–2599

ION 2 – Calculates the Distribution of Ions around Biomolecules

ION 2

:: DESCRIPTION

The ION software determines the distribution of ions around biomolecules using the Poisson model and Metropolis Monte-Carlo algorithm.

::DEVELOPER

Biomolecular Machines Laboratory 

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ION

:: MORE INFORMATION