Molecular Science Software

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Molecular Science Software

  • Focus on your Business with an integrated Business Cloud Focus on your Business with an integrated Business Cloud Icon
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  • Command line tool to edit xyz files

    It is a commandline tool to manipulate .xyz molecule files.

    Downloads: 0 This Week Last Update: See Project
  • 20best

    A small python tool to read PDB files from CNSsolve calculations and sort the by the total energy of the structure.

    Downloads: 0 This Week Last Update: See Project
  • 2D HF

    This is an extension to the standard 2D HF package (A Numerical Hartree-Fock Program for Diatomic Molecules by Jacek Kobus, Leif Laaksonen and Dage Sundholm) that adds some extra functionality.

    Downloads: 0 This Week Last Update: See Project
  • 2DFLT Icon

    2DFLT

    Program for Normalization, Averaging and Editing of In Situ Data Sets

    2DFLT it is first out of two programs which allows implementation of Phase Sensitive Detection (PSD) and/or Modulated Enhanced Diffraction (MED) techniques on the in situ data. This software allows collecting individual data files from in situ experiment into one dataset. After that this data set can be visualized, edited, normalized and averaged. Resulted data can be saved as one flat file (FLT-format) which can be used for PSD/MED calculations via 2DMED software (http://sourceforge.net/projects/twodmed/?source=directory). 2DFLT specifically was written to target in situ X-ray Powder Diffraction data from synchrotron measurements. Hence it can read CHI, XYE (TOPAS), FXYE(GSAS/ GSASII) and XY- files formats. However it can read general in situ data written into individual TXT or XY – files.

    Downloads: 0 This Week Last Update: See Project
  • 2DMED Icon

    2DMED

    Phase Sensitive Detection and Modulated Enhanced Diffraction Software

    2DMED it is the second out of two programs which allows implementation of Phase Sensitive Detection (PSD) and/or Modulated Enhanced Diffraction (MED) techniques on the in situ data. This software takes normalized and averaged in situ data in flat file format (FLT) and performs PSD transformation which has been described in Urakawa, A.et al. Chem. Eng. Science 2008, 63, 4902. User can choose demodulation index k and perform several demodulation calculations. This is extremely important since demodulation calculations at k = 2 on in situ powder diffraction data represent implementation of MED method which been described in Chernyshov, D. et al. Acta Cryst. 2011, A67, 327. Demodulated data can be then viewed on 2D and/or 1D plot and analyses with different tools including In Phase Plot, Maximum Amplitude Plot and Positive Pattern Plot. Demodulated data also can be saved in ASCII format for further analysis.

    Downloads: 0 This Week Last Update: See Project
  • 4DiCeS

    4-Dimensional Cell Simulator (4DiCeS) is a framework on hybrid (stochastic and deterministic) modeling and simulation of (whole) cell environments in 4D. The framework may incorporate any reaction and diffusion algorithms applicable in a 4D grid layout.

    Downloads: 1 This Week Last Update: See Project
  • ABFF Icon

    ABFF

    Project for develop force fields with using ab-initio calculations

  • ABIFManager

    Program for editing of ABIF formated files

    Downloads: 2 This Week Last Update: See Project
  • AMORSS: redox enzymes simulation system

    This project is A Mitochondrial OxydoReduction Simulation System. It consists of two linked projects: a program for displaying and analysing large biomolecular systems (Floral) and a multi-agent simulator for biomolecular oxydoreduction systems (AMORSS).

    Downloads: 0 This Week Last Update: See Project
  • ANT.Gaussian

    Quantum transport code based on Gaussian03/09

    Atomistic NanoTransport (ANT) comprises a series of codes designed to compute electronic quantum transport with a broad range of applicability in nanoelectronics. ANT.Gaussian (or ANT.G for brevity) relies on the popular quantum chemistry code GAUSSIAN03/09 code with which interfaces in a seamless manner. Straightforwad use of ANT.G include the computation of the zero-bias conductance (or, alternatively, the electrical current under an applied bias voltage) of a variety of nanoscale systems such as molecular bridges or simply metallic atomic contacts as those created with scanning tunneling microscope or break junction techniques. The use of ANT.G may also be naturally extended to the computation of scanning tunneling spectroscopy and the simulation of scanning tunneling and electrostatic force microscopy.

    Downloads: 0 This Week Last Update: See Project
  • APBS Icon

    APBS

    APBS is a software package for the numerical solution of the Poisson-Boltzmann equation, a popular continuum model for describing electrostatic interactions between molecular solutes over a wide range of length scales. <http://www.poissonboltzmann.org/>. Please register at http://goo.gl/LGVU5j before downloading!

  • APBSmem

    APBSmem is a Java-based graphical user interface for Poisson-Boltzmann electrostatics calculations at the membrane. APBS version 1.2.0 or later is required.

    Downloads: 6 This Week Last Update: See Project
  • Able Opus Elements Icon

    Able Opus Elements

    An interactive periodic table of elements, with a Bohr Model generator

    The core of this program is a interactive periodic table of elements but also has a handful of goodies Including: A bohr model generator, a nice mix & match memory game, a nifty find dialog. The periodic table is built for quick lookup of basic info

    Downloads: 0 This Week Last Update: See Project
  • Agent-Based Multiscale Tissue Model

    Agent-based multiscale model of cancer proliferation dynamics

    Downloads: 0 This Week Last Update: See Project
  • Allelome.PRO

    A pipeline to define allele-specific genomic features

    Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here we present Allelome.PRO, an automated userfriendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analysed imprinted expression to give a complete picture of the “allelome” by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased biallelic or noninformative. Allelome.PRO offers increased sensitivity to analyse lowly expressed transcripts, together with a robust false discovery rate empirically calculated from variation in the sequencing data.

    Downloads: 0 This Week Last Update: See Project
  • AnharmoniCAOS

    Cagliari-Orsay model for anharmonic molecular spectra in 2nd order PT

    Given dynamical coefficients and/or derivatives of the ionic potential with respect to normal (harmonic) vibrational modes, compute anharmonic energies and electric dipole-permitted transitions and intensities using nearly-degenerate perturbation theory (i.e. properly accounting for Fermi and Darling-Dennison resonances).

    Downloads: 0 This Week Last Update: See Project
  • Ascalaph Designer Icon

    Ascalaph Designer

    Graphic molecular dynamic package.

    Molecular Graphics, Molecular Dynamics, Optimization, Quantum chemistry. Molecular model building. Explicit and implicit water models. http://www.biomolecular-modeling.com/Products.html

  • Assembly of mixed genomes

    Scripts used to assemble and deconvolute mixed mitochondrial genomes.

    Perl scripts used in the paper "Index-free de novo assembly and deconvolution of mixed mitochondrial genomes" by McComish BJ, Hills SFK, Biggs P and Penny D (2010) Genome Biology and Evolution 2:410-424.

    Downloads: 0 This Week Last Update: See Project
  • Atomic Global Minimum Locator

    This software searches the potential energy surface of small to medium size atomic systems for global minima using quantum ab initio techniques. It performs bond rotations and molecule translations and rotations on a Linux cluster with MPI.

  • Atomic-Clusters

    This project is intended to perform Monte-Carlo-Simulations to calculate small clusters (2 to 13 atoms) of the rare gas "argon".

    Downloads: 0 This Week Last Update: See Project
  • Autmated Peptide Screening

    Screening peptides for MHC and/or MHC-T cell receptor affinity

    Modified version of AutoGrow, autogrow.ucsd.edu/ , with a mutation script added in the class files, and a global change of the defined mutation point from Hydrogen atoms to Calphas, to allow placement of Amino Acids. Deposited are 3 versions, used for my PhD Thesis. These allow for mutation of short 2-15 amino acid peptides, and associated screening of these using AutoDock or AutoDock Vina, allowing for 8 CPU systems to screen 10K peptides a day or 1-2K with flexible residues added in. A detailed method for determining the peptide ligand for any sequenced and modeled T cell receptor will be published and link added at some point. These scripts are written quickly in a couple weeks to meet a task and could be re-written more eloquently. I may or may not work on this project again, the goal would be to introduce amino acids into any protein in openCL to allow automated design on GPU's.Limits-The standard PDB codes used slightly modified, proline not at angles, peptide shld be linear,

    Downloads: 0 This Week Last Update: See Project
  • AutoDock Software in Parallel with GPUs

    Using the CUDA API this project modifies the AutoDock software to run in parallel on NVIDIA GPUs. Users will be able to download and compile the code and use AutoDock on CUDA capable Graphics Cards. Autodock is located at http://autodock.scripps.edu/

    Downloads: 9 This Week Last Update: See Project
  • AutoLabToolkit

    Tools for automating everyday laboratory tasks

    Tools for automating everyday laboratory tasks. Imaging and informatics tools for biological research.

    Downloads: 0 This Week Last Update: See Project
  • AutoShim

    Tools to build molecular-docking activity prediction models by PLS regression with iterative training and pose-selection. Descriptors include (i) docking score(s), (ii) pharmacophore features, (iii) multi-feature descriptors learned by decision trees.

    Downloads: 0 This Week Last Update: See Project
  • Avogadro Icon

    Avogadro

    An intuitive molecular editor and visualization tool

    Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. It offers a flexible rendering framework and a powerful plugin architecture.

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