MEGA 10.0 – Molecular Evolutionary Genetics Analysis

MEGA 10.0

:: DESCRIPTION

MEGA (Molecular Evolutionary Genetics Analysis)is an integrated tool for automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses.

::DEVELOPER

MEGA Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX

:: DOWNLOAD

MEGA

:: MORE INFORMATION

Citation

Mol Biol Evol. 2013 Dec;30(12):2725-9. doi: 10.1093/molbev/mst197. Epub 2013 Oct 16.
MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S.

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, and Kumar S (2011)
MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods.
Molecular Biology and Evolution (2011)doi: 10.1093/molbev/msr121 First published online: May 4, 2011

GROMACS 2019.4 – Molecular Simulation

GROMACS 2019.4

:: DESCRIPTION

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

::DEVELOPER

GROMACS Team 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 GROMACS

:: MORE INFORMATION

Citation

Hess, et al. (2008)
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
J. Chem. Theory Comput. 4: 435-447.

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.
Pronk S, Páll S, Schulz R, Larsson P, Bjelkmar P, Apostolov R, Shirts MR, Smith JC, Kasson PM, van der Spoel D, Hess B, Lindahl E.
Bioinformatics (2013) 29 (7): 845-854.

AmberTools 14 – Molecular Dynamics Simulation

AmberTools 14

:: DESCRIPTION

AmberTools consists of several independently developed packages that work well by themselves, and with Amber (Assisted Model Building with Energy Refinement) itself. The suite can also be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB), with generalized Born solvent models.

AmberTools consists of 7 main codes
NAB build molecules; run MD or distance geometry, using generalized Born, Poisson-Boltzmann or 3D-RISM implicit solvent models
antechamber Create force fields for general organic molecules
ptraj Analyze trajectories from Amber or CHARMM
tleap and xleap Basic preparation program for Amber simulations
sleap replaces and expands tleap
sqm semiempirical and DFTB quantum chemistry program
pbsa Performs numerical solutions to Poisson-Boltzmann models

::DEVELOPER

AMBER Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  MacOsX / Window with Cygwin

:: DOWNLOAD

AmberTools

:: MORE INFORMATION

Citation

D.A. Case, T.E. Cheatham, III, T. Darden, H. Gohlke, R. Luo, K.M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang and R. Woods.
The Amber biomolecular simulation programs.
J. Computat. Chem. 26, 1668-1688 (2005).

Vesimulus 2.1 – Molecular Stochastic Simulations of Metabolic or Signaling Systems

Vesimulus 2.1

:: DESCRIPTION

Vesimulus is a simulation package for molecular stochastic simulations of metabolic or regulatory biological systems.

::DEVELOPER

Chair of Computational Biology at the Saarland University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 Vesimulus

:: MORE INFORMATION

Citation

PLoS One. 2010 Nov 22;5(11):e14070. doi: 10.1371/journal.pone.0014070.
Bridging the gap: linking molecular simulations and systemic descriptions of cellular compartments.
Geyer T, Mol X, Blass S, Helms V.

Surface Racer 5.0 – Calculation of Accessible and Molecular Surface Areas and Average Surface Curvature

Surface Racer 5.0

:: DESCRIPTION

Surface Racer calculates exact accessible surface area, molecular surface area and average curvature of molecular surface for macromolecules. The program also analyzes cavities in the protein interior inaccessible to solvent from outside. The output includes the surface parameters for each residue in addition to those for individual atoms.

DEVELOPER

Tsodikov laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

  Surface Racer

:: MORE INFORMATION

Citation

Tsodikov, O. V., Record, M. T. Jr. and Sergeev, Y. V. (2002).
A novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature.
J. Comput. Chem., 23, 600-609.

Rasmol 2.7.5.2 – Molecular Graphics Visualisation

Rasmol 2.7.5.2

:: DESCRIPTION

RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images.

The program reads in molecular coordinate files and interactively displays the molecule on the screen in a variety of representations and colour schemes. Supported input file formats include Protein Data Bank (PDB), Tripos Associates’ Alchemy and Sybyl Mol2 formats, Molecular Design Limited’s (MDL) Mol file format, Minnesota Supercomputer Center’s (MSC) XYZ (XMol) format, CHARMm format, CIF format and mmCIF format files. It displays the molecule in various representations and allows one to rotate the molecule interactively.

::DEVELOPER

The gforge OpenRasMol project

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/MacOsX/Linux

:: DOWNLOAD

RasMol

:: MORE INFORMATION

Future releases of RasMol will continue to offer the GPL and RASLIC as alternative licenses for the source code, but, in order to conform to the license conditions of various libraries to which executables may be linked, starting with RasMol 2.7.5 release, the GPL is the only valid license to use the binary distributions.

MolScript 2.1.2 – Display Molecular 3D Structures

MolScript 2.1.2

:: DESCRIPTION

MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations.The user supplies an input file (the script) which specifies the coordinate file, what objects to render and the exact appearance of the objects through the graphics state parameters.

::DEVELOPER

Per Kraulis

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • SGI IRIX / Linux

:: DOWNLOAD

 MolScript

:: MORE INFORMATION

Citation

P. J. Kraulis,
MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures
Journal of Applied Crystallography (1991) v 24, pp 946-950.

SeqAssem 200807- Molecular Sequence Assembly

SeqAssem 200807

:: DESCRIPTION

SeqAssem is a molecular sequence assembly software, proof-reading of trace file data, contig building …..

::DEVELOPER

SequentiX

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

SeqAssem

:: MORE INFORMATION

Request a free trial license to use the full spectrum of features for one month and free of charge!

MASKER – Molecular Surface Area Calculator

MASKER

:: DESCRIPTION

MASKER is a program for calculating solvent accessible surface (SAS)  solvent excluded surface (SES) and solvation energy. Three program that use the MASKER module are included in this package:

pdbmask — calculates the solvent excluded surface of atoms in PDB format
maskercm — calculates the pairwise buried surface of residues in a protein
voidmask — finds the locations of buried empty spaces with in a protein, or any molecule.

MASKER contact map server

MASKER buried void calculator

::DEVELOPER

Chris Bystroff

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

MASKER

:: MORE INFORMATION

Citaiton

C. Bystroff (2002)
MASKER: Improved solvent excluded molecular surface area estimations using Boolean masks
Protein Engineering, 15:959-965

Desmond 2.4 – High-speed Molecular Dynamics Simulation

Desmond 2.4

:: DESCRIPTION

Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters. The code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms containing a large number of processors, but may also be executed on a single computer.

::DEVELOPER

D. E. Shaw Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Window / Linux / Mac OsX
  • Python

:: DOWNLOAD

Desmond

:: MORE INFORMATION

Citation

Kevin J. Bowers, Edmond Chow, Huafeng Xu, Ron O. Dror, Michael P. Eastwood, Brent A. Gregersen, John L. Klepeis, István Kolossváry, Mark A. Moraes, Federico D. Sacerdoti, John K. Salmon, Yibing Shan, and David E. Shaw,
Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters,”
Proceedings of the ACM/IEEE Conference on Supercomputing (SC06), Tampa, Florida, November 11–17, 2006