Tag: Program

MDynaMix 5.2.8 – Molecular Dynamics Program

MDynaMix 5.2.8

:: DESCRIPTION

MDynaMix is a general purpose molecular dynamics code for simulations of mixtures of either rigid or flexible molecules, interacting by a force field consisting of Lennard-Jones, electrostatic, covalent bonds, angles and torsion angles potentials as well as of some optional terms, in a periodic rectangular, hexagonal or truncated octahedron cell. Rigid bonds are constrained by the SHAKE algorithm. In case of flexible molecular models the double time step algorithm is used. Algorithms for NVE, NVT and NPT statistical ensembles are implemented, as well as Ewald sum for treatment of the electrostatic interactions. Treatment of quantum correction to the atomic motion can be done within the Path Integral Molecular Dynamics approach. Possibility for free energy computations by the expanded ensemble method is included.

::DEVELOPER

Lyubartsev, Alexander

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  MDynaMix

:: MORE INFORMATION

Citation

A.P.Lyubartsev, A.Laaksonen,
MDynaMix – A scalable portable parallel MD simulation package for arbitrary molecular mixtures”
Computer Physics Communications, 128, 565-589 (2000).

LSJuicer 0.2rc2 – Program for Squeezing Results from Linescan images

LSJuicer 0.2rc2

:: DESCRIPTION

LSJuicer is a multi-platform tool for analysing fluorescence vs. time data (e.g. linescan images from confocal microscopes, csv data from spectrophotometers, fluorimeters, etc)

::DEVELOPER

Laboratory of Systems Biology at Institute of Cybernetics

:: SCREENSHOTS

LSJuicer

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python
  • Java

:: DOWNLOAD

 LSJuicer

:: MORE INFORMATION

ProAlign 0.5a3 – Probabilistic Multiple Alignment program

ProAlign 0.5a3

:: DESCRIPTION

ProAlign is a software implementing a multiple-alignment method that combines a Hidden Markov model (HMM), a progressive alignment algorithm, and a probabilistic character substitution model. Check below for much additional information.

::DEVELOPER

Michel C. Milinkovitch’s lab

:: SCREENSHOTS

:: REQUIREMENTS

  • MacOsX / Linux / Windows
  • Java

:: DOWNLOAD

 ProAlign

:: MORE INFORMATION

Citation

Ari Löytynoja and Michel C. Milinkovitch*
A hidden Markov model for progressive multiple alignment
Bioinformatics, 19:1505-1513 (2003)

GenSeed 1.0.22 – Seed-driven progressive Assembly program

GenSeed 1.0.22

:: DESCRIPTION

GenSeed is a Perl program that implements a seed-driven recursive assembly consisting of cycles comprising a similarity search, read selection and assembly. The iterative process results in a progressive extension of the original seed sequence.

::DEVELOPER

GenSeed Team 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GenSeed

:: MORE INFORMATION

Citation:

Sobreira, T.J.P. & Gruber, A. (2008).
Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data.
Bioinformatics, doi: 10.1093/bioinformatics/btn283

TRAP 1.1 – Tandem Repeats Analysis Program

TRAP 1.1

:: DESCRIPTION

TRAP is a Perl program that provides a unified set of analyses for the selection, classification, quantification and automated annotation of tandemly repeated sequences.

::DEVELOPER

TRAP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 TRAP

:: MORE INFORMATION

Citation:

Sobreira, T.J.; Durham, A.M. & Gruber, A. (2006).
TRAP: automated classification, quantification and annotation of tandemly repeated sequences.
Bioinformatics 22(3): 361-362.

RNASEQR 1.0.2 – Streamlined and Accurate RNA-seq Sequence Analysis program

RNASEQR 1.0.2

:: DESCRIPTION

RNASEQR is a nucleotide sequence mapper/aligner and is designed specifically for RNA-seq data analysis. It takes advantage of annotated transcripts and genomic reference sequences to obtain high quality mapping/alignment results.

::DEVELOPER

Hood Lab at ISB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  RNASEQR

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Mar;40(6):e42. Epub 2011 Dec 22.
RNASEQR–a streamlined and accurate RNA-seq sequence analysis program.
Chen LY, Wei KC, Huang AC, Wang K, Huang CY, Yi D, Tang CY, Galas DJ, Hood LE.

ABE 1.0 – Bioassay Analysis program

ABE 1.0

:: DESCRIPTION

ABE is a small, fast and convenient program for visualizing and modeling experimental bioassay data. The data can be modeled using either polynomials or a more specific four-parameter model based upon the standard, sigmoidal dose-response curve.

::DEVELOPER

Gordon Webster, EMD Lexigen Research Center

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Python

:: DOWNLOAD

 ABE

:: MORE INFORMATION

Elves 1.3.6.1.2 – Conversational User Interface to the most common X-ray Crystallography programs

Elves 1.3.6.1.2

:: DESCRIPTION

Elves are a compact, portable, and intelligent “conversational user interface” to the most common X-ray crystallography programs like CCP4, mosflm, denzo, solve, and shelx. Elves exist as a single text file (shell script) which will run on any unix platform using nothing more than basic unix utilities like csh, awk and grep (plus the executables of the public-domain X-ray programs). Users communicate with the Elves in plain english, and the Elves will then locate, set up and run the appropriate x-ray programs.

::DEVELOPER

James Holton

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Elves

:: MORE INFORMATION

Citation

Holton, J. M. & Alber, T. (2004)
Automated protein crystal structure determination using ELVES
Proc. Natl. Acad. Sci. USA 101, 1537–1542.

XtalView 4.0 – Molecular Graphics Program

XtalView 4.0

:: DESCRIPTION

XtalView is a complete package for solving a macromolecular crystal structure by isomorphous replacement, including building the molecular model. It runs on Sun, DEC, SGI, IBM and PC/Linux computers and takes full advantage of the modern workstation environment. It has a simple but comprehensive windows based interface. The xtalmgr, the main menu drives a suite of crystallographic modules by click of an icon. XtalView maintains log files of the computations done. Standard file formats are used, which facilitates communication between XtalView and programs such as CCP4, X-PLOR, TNT, and MERLOT.

::DEVELOPER

Duncan McRee

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

   XtalView

:: MORE INFORMATION

Citation

McRee, D.E. (1999)
XtalView/Xfit – A Versatile Program for Manipulating Atomic Coordinates and Electron Density.
Journal Structural Biology, vol. 125, pp. 156-165.

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