iMODFIT 1.51 – Fitting of Atomic Structures into EM maps based on iMOD

iMODFIT 1.51

:: 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

  • Windows / Linux

:: DOWNLOAD

 iMODFIT

:: 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.

ADP_EM 2.1 – Fast Rigid-body Fitting

ADP_EM 2.1

:: 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

  • Windows / Linux

:: DOWNLOAD

 ADP_EM

:: 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

ProFit 3.1 – Protein Least Squares Fitting

ProFit 3.1

:: 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.

ProFit Online Version

::DEVELOPER

Andrew C.R. Martin’s Bioinformatics Group at UCL

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows

:: DOWNLOAD

 ProFit

:: MORE INFORMATION

BioNetFit – Fitting tool for Rule-based Models

BioNetFit 1.0

:: DESCRIPTION

BioNetFit is a general-purpose fitting program for rule-based models that is compatible with BioNetGen and NFsim

::DEVELOPER

BioNetFit team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 BioNetFit

:: 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.

GeneRave 3.0.9 – Fitting Sparse Response Models to very high Dimensional data

GeneRave 3.0.9

:: DESCRIPTION

GeneRave is an R package designed for fitting sparse response models to very high dimensional data.

::DEVELOPER

CSIRO Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

GeneRave

:: 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.

sparse.inv.cov 1.0.4 – Fitting very large Sparse Gaussian Graphical Models

sparse.inv.cov 1.0.4

:: DESCRIPTION

sparse.inv.cov is an R package designed for fitting large sparse covariance selection models.

::DEVELOPER

CSIRO Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R

:: DOWNLOAD

 sparse.inv.cov

:: 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

MultiFit – Fitting of Multiple Proteins into their Assembly Density Map

MultiFit

:: 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

Andrej Sali Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: 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.

CCOptimF – R code for fitting Random Periods Model

CCOptimF

:: DESCRIPTION

CCOptimF is a software for fitting the Random Periods Model (RPM) for cell cycle genes.

::DEVELOPER

Shyamal D. Peddada, Ph.D. 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CCOptimF

:: MORE INFORMATION

Citation

Liu D, Umbach D, Peddada SD, Li L, Crockett P and Weinberg C (2004).
A Random-Periods Model for Expression of Cell-Cycle Genes.
Proceedings of National Academy of Sciences, 101, No. 19, 7240-7245.

vBsr 0.0.1 – Fitting an Ultra-sparse Variational Bayes Spike Regression model

vBsr 0.0.1

:: 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

Charles Kooperberg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 vBsr

:: 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).

Flex-EM – Fitting and Refinement of Atomic Structures

Flex-EM

:: 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

Andrej Sali Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  Flex-EM

:: 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