Tag: Biomolecule

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

SMOG 2.4.2 / OpenSMOG 1.1 – Structure-based Models for Biomolecules

SMOG 2.4.2 / OpenSMOG 1.1

:: 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.

OpenSMOG : Simulating SMOG models in OpenMM

::DEVELOPER

SMOG team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SMOG / OpenSMOG

:: MORE INFORMATION

Citation

de Oliveira AB Jr, Contessoto VG, Hassan A, Byju S, Wang A, Wang Y, Dodero-Rojas E, Mohanty U, Noel JK, Onuchic JN, Whitford PC.
SMOG 2 and OpenSMOG: Extending the limits of structure-based models.
Protein Sci. 2021 Oct 16. doi: 10.1002/pro.4209. Epub ahead of print. PMID: 34655449.

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

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.