Search Results for "c:\program files\micronetics\msmws\program\" - Page 3
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Showing 77 open source projects for "c:\program files\micronetics\msmws\program\"
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mobcalPARSER
A cross-platform interface for the *.mfj file format.
mobcalPARSER is a command line based PERL frontend/interface for MOBCAL with limited wrapper functionality. "MOBCAL - A Program to Calculate Mobilities" is available from Professor Martin F. Jarrold's webpage http://www.indiana.edu/~nano/software.html. -
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TrajLab
MATLAB based programs for trajectory simulations of molecules
...While the authors are aware that many other highly specialized and highly optimized program packages for the same purpose exist (e. g. AMBER, GROMACS, NAMD, etc.), the MATLAB environment offers easy access to manipulating the codes, testing novel algorithms, non-standard force fields and performing all kinds of numerical experiments. To be used mainly in teaching! -
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Primer Design Tool
Design PCR primers
A simple tool to design DNA primers for mutagenesis in BGME lab (JHU). Allows users to select or enter background sequence and add current and new mutations. During the design process, users are presented with various updating checks to guide them. -
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SMMP (Simple Molecular Mechanics for Proteins) is a program library for protein simulations with an emphasis on advanced Monte Carlo algorithms. It includes various force fields to calculate the energy of a protein and protein-protein interactions.
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A GUI program to create the plasmid database forms for BGME lab. This program presents user with a data entry form for entering plasmid information and automatically converts DNA sequence to protein, aligns it, and creates text output file.
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Smoldyn is a computer program for simulating reactions and diffusion at a mesoscopic size scale. This scale lies between the more traditional microscopic size scale, in which all or most atoms are considered.
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PySpline is a graphical, cross-platform program for processing X-ray absorption spectroscopy (XAS) and Extended X-ray absorption fine structure (EXAFS) data. It allows processing parameters to be adjusted and observe the effect on R-space data.
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This is a set of scripts that helps with processing of NMR pH titration data. These scripts allow for fitting (using R) and plotting of data of multiple residues. The program needs to be made more user friendly.
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The sibRNAfold program is a modification of the Vienna RNAfold program for RNA secondary structure prediction through energy minimization.
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The Fortran program MOLLY generates atomic positions in a molecule from those of a small number of prototype atoms and the molecule's point symmetry. It is intended as a time-saving aid in preparing input data for computational physics software.
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The project devoted to develop LADY software. LADY is a abbreviation formed from LAttice DYnamics toolkit. The software is the semi-emperical program which aids to simulate the dynamical property of crystals within a selected potential function.
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FGH is program that solves vibrational Schroedinger equation using the Fourier grid hamiltonian method. The program requires potential energy surface and G-matrix defined at the uniform grid of points.
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SDFCherry is a command-line program that searches for textual matches in molecular structure files of SDF format and outputs the structures that match. Optionally adds a data field to the matched structures, e.g., biological activity. Useful for QSAR.
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Shape is a molecular conformation prediction program. It uses a genetic algorithm to efficiently search the conformational space of a biomolecule and then clusters the results. It is very simple to use.
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ProteinShader is a molecular visualization tool that can produce illustrative renderings of proteins that approximate what an artist might create using pen and ink. This free platform-independent program is written in Java and OpenGL Shading Language.
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TARIS (Tree Analysis and Representation of Isopotential Surfaces) is a software package designed for molecular similarity purposes in the field of Computational Chemistry. Users are allowed to compare molecules through their MEP loading .cube files.
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This program simulates the performance of the supersonic continuous wave chemical laser by solving 2D-system of Navier-Stokes equations in slender-jet approximation that includes multi-component diffusion, non-equilibrium chemical reactions and radiation
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The program NAcMoS (Nucleic Acid Modeling System) is a software package that leads to a natural classification of RNAs represented as weighted graphs.
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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).
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Tautomer generator is a program that generates a set of molecules (tautomers) from a molecular core and number of hydrogen atoms.
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PyMOlyze is a graphical program to analyze the results of quantum chemistry (HF/DFT) calculations. Features include various population analyses, fragment analysis, monitoring structures during an optimization, and a simple, but powerful, XYZ editor.
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OOPS means Open Protein Simulator, it is a program designed to serve as a test bed for different algorithms for protein folding, dynamics and structure prediction. OOPS is based on a plugin architecture that makes it highly modular and extensible.
