:: DESCRIPTION
sparse.inv.cov is an R package designed for fitting large sparse covariance selection models.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Harri Kiiveri, Frank de Hoog
Fitting very large sparse Gaussian graphical models
Computational Statistics & Data Analysis Volume 56, Issue 9, September 2012, Pages 2626–2636
:: DESCRIPTION
MultiFit is a computational method for simultaneously fitting atomic structures of components into their assembly density map at resolutions as low as 25 Å. The component positions and orientations are optimized with respect to a scoring function that includes the quality-of-fit of components in the map, the protrusion of components from the map envelope, as well as the shape complementarity between pairs of components. The scoring function is optimized by an exact inference optimizer DOMINO that efficiently finds the global minimum in a discrete sampling space.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W167-70. doi: 10.1093/nar/gkr490.
MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map.
Tjioe E1, Lasker K, Webb B, Wolfson HJ, Sali A.
:: DESCRIPTION
Flex-EM includes a rigid fitting stage followed by a refinement stage. Rigid fitting can be performed with Mod-EM or any other rigid fitting methods. The refinement stage starts with the components rigidly fitted in the approximate positions in the map. Two methods are available: conjugate gradients minimization (CG) and simulated annealing molecular dynamics (MD).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
M. Topf, K. Lasker, B. Webb, H. Wolfson, W. Chiu, A. Sali.
Protein Structure Fitting and Refinement Guided by Cryo-EM Density
Structure 16, 295-307, 2008
:: DESCRIPTION
BioNetFit is a general-purpose fitting program for rule-based models that is compatible with BioNetGen and NFsim
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BioNetFit: a fitting tool compatible with BioNetGen, NFsim, and distributed computing environments.
Thomas BR, Chylek LA, Colvin J, Sirimulla S, Clayton AH, Hlavacek WS, Posner RG.
Bioinformatics. 2015 Nov 9. pii: btv655.
:: DESCRIPTION
GeneRave is an R package designed for fitting sparse response models to very high dimensional data.
::DEVELOPER
CSIRO Transformational Bioinformatics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2008 Apr 15;9:195. doi: 10.1186/1471-2105-9-195.
A general approach to simultaneous model fitting and variable elimination in response models for biological data with many more variables than observations.
Kiiveri HT.
:: DESCRIPTION
BGFit provides a web-based unified platform, where a rich set of dynamic models can be fitted to experimental time-series data, further allowing to efficiently manage the results in a structured and hierarchical way.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Veríssimo A, Paixão L, Neves AR, Vinga S.
BGFit: management and automated fitting of biological growth curves.
BMC Bioinformatics. 2013 Sep 25;14:283. doi: 10.1186/1471-2105-14-283. PMID: 24067087; PMCID: PMC3848918.
:: DESCRIPTION
ADP_EM (Another Docking Platform for EM) is ultra fast multiresolution fitting tool which has been specially designed to support high throughput coverage. The method uses spherical harmonics to effectively speed up the rotational scan.
::DEVELOPER
The Structural Bioinformatics Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Jose Ignacio Garzón, Julio A. Kovacs, Ruben Abagyan, and P. Chacón. (2007)
ADP_EM: Fast exhaustive multi-resolution docking for high-throughput coverage.
Bioinformatics. 23(4):427-33
:: DESCRIPTION
iMODFIT is an efficient tool for flexible fitting of atomic structures into EM maps based on Normal Mode Analysis in internal Coordinates.
::DEVELOPER
The Structural Bioinformatics Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Struct Biol. 2013 Aug 30. pii: S1047-8477(13)00216-5. doi: 10.1016/j.jsb.2013.08.010.
iMODFIT: Efficient and robust flexible fitting based on vibrational analysis in internal coordinates.
Lopéz-Blanco JR, Chacón P.
:: DESCRIPTION
ProFit is designed to be the ultimate program for performing least squares fits of two or more protein structures. It performs a very simple and basic function, but allows as much flexibility as possible in performing this procedure.
::DEVELOPER
Andrew C.R. Martin’s Bioinformatics Group at UCL
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
vBsr (Variational Bayes Spike Regression model) is the code for fitting an ultra-sparse variational Bayes spike regression model, with applications to Genome-wide association studies
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Code is in an early release form (version 0.0.1), and details of the model are forthcoming. Email questions to Ben Logsdon (blogsdon@fhcrc.org).