Open Source Mac Chemistry Software - Page 5

BioNLP-Corpora is a repository of biomedically and linguistically annotated corpora and biomedical data sources. There are many resources available in separate packages in this project.

This software can be used to calculate thermochemical and kinetic quantities like, enthalpy, entropy, heat capacity and transition state theory rate constants from spectroscopic/quantum data.

Canvas-2DGC is a user-extensible, Freemat based 1DGC and comprehensive 2DGC (GCxGC) data visualization and processing software. GCxGC-MS data analysis is supported for Agilent GCMS data format. The first goal of this project is to provide a highly intelligent analytical tool for reducing a complex chromatographic data analysis, either 1D or 2D, to just a few simple and intuitive steps. The second goal is to provide a fast and practical way of customizing or extending functionalities by ordinary users through high-level Freemat scripting. Freemat, one of open source Matlab clones, is chosen for this very purpose, because its syntax is most compatible with Matlab and it is lightweight - very suited for ordinary users. Contact xguan@jnxtec.com for support.

Charmol is a cross-platform GUI/command-line based program for making high-quality pictures of molecular structures, nowadays working on Linux, MacOS and Windows. As output, it produces POV-Ray rendered images or files in VRML format. Charmol is capable of making pictures containing: - from small- to large-size molecules - more molecules together (different settings possible) - orbitals using molden and fchk files (GTO functions up to 'h' angular momentum supported) - surfaces using gaussian cube files (also color-mapped surfaces according to potential) - schematic representation of vibrations using arrows - user-defined arrows representing vectorial properties - measuring gauges - combinations of these features (more orbitals together, orbitals and arrows together etc.) Charmol allows for fine tuning of the final molecular design.

Frowns is a chemoinformatics system written almost entirely in python.

"GEnerator of atomic COORdinates for armchair nanotubes with specific bond lengths and angles. (gecoor) Gustavo Domínguez Rodríguez, Gabriel Iván Canto Santana, Jorge Alejandro Tapia Gonzalez, Cesar Alberto Cab Cauich A problem that arises when applying specific strain fields to nanostructures is knowing the atomic coordinate positions that produce the required structural parameters, such as bond lengths and angles. Due to this, a simple-to-use program is implemented within a command-line, for both Linux and MS Windows environments, to generate atomic coordinate files for later use in first-principles simulation codes. The program considers monatomic armchair nanotubes, and the geometric parameters considered are: the length of the bonds perpendicular to the tube axis, the length of the non-perpendicular bonds, and the angle between two non-perpendicular bonds."

The JCAMP-DX project is the reference implemention of the IUPAC JCAMP-DX spectroscopy data standard.

The Maltcms - Modular Application Toolkit for Chromatography Mass-Spectrometry is a JAVA API for preprocessing, alignment, analysis and visualization of data stored in open file formats used in Proteomics and Metabolomics research.

Mole (Chemistry Calculator) can calculate molar mass, number of moles and atoms, empirical and molar formulas and can do stoichiometric calculations such as percent yield and limiting reactant. Mole can also do gas stoichiometry and gas law calculations.

NMRShiftDB is an open-source, open-access, open-submission, open-content web database for chemical structures and their nuclear magnetic resonance data.

OpenDinTest is a OpenOffice-Calc-Sheet for statistical Data-Analysis according to the german industry-norm DIN 32645. <br> <br> OpenDinTest ist eine OpenOffice-Calc-Datei zur statistischen Auswertung von Messdaten nach der DIN 32645. <br>

OBExtensions is a extension library for the chemoinformatics library Openbabel. It provides extensions to Openbabel, being mostly GUI widgets. OBExtensions has a 2D/3D viewer, 2D coordinates generator and some other extensions.

ProtoFit is software for modeling the acid/base behavior of surfaces. The software is used for parameterizing surface protonation models and for visualization of potentiometric titration data.

PyMOL Plugins aims to provide many plugins for the PyMOL software. You can find further informations about PyMOL on this website: http://www.pymol.org/

RASP uses structure-based chemical shift predictions to solve the backbone resonance assignment problem in protein NMR spectroscopy. This enables rapid determination of highly accurate assignments on the basis of minimal experimental datasets, even for spectroscopically challenging proteins. RASP takes as input spin systems assembled on the basis of an arbitrary set of conventional triple-resonance NMR experiments. Uniquely, RASP is capable of extensive assignments even in the abscence of Cbeta chemical shift information: over a test set of 154 proteins RASP assigns 88 % of residues with an accuracy of 99.7 %, using only information available from HNCO and HNCA spectra. RASP is described here: MacRaild and Norton (2014) RASP: Rapid and robust backbone chemical shift assignments from protein structure. J Biomol NMR doi:10.1007/s10858-014-9813-7

Data visualization, generate metadata log files, save spectra in .txt format for further advanced analysis.

Bioinformatics related demos and tutorials using the R programming language for large biological data. Licence: Creative Commons Attribution-NonCommercial 4.0 International License

UPDATE: LATEST VERSION AT http://git.durrantlab.com//jdurrant/wisp Allostery can occur by way of subtle cooperation among protein residues (e.g., amino acids) even in the absence of large conformational shifts. Dynamical network analysis has been used to model this cooperation, helping to computationally explain how binding to an allosteric site can impact the behavior of a primary site often many angstroms away. Traditionally, computational efforts have focused on the most optimal path of correlated motions leading from the allosteric to the primary active site. We present a program called Weighted Implementation of Suboptimal Paths (WISP) capable of rapidly identifying additional suboptimal pathways that may also play important roles in the transmission of allosteric signals. Aside from providing signal redundancy, suboptimal paths traverse residues that, if disrupted through pharmacological or mutational means, could modulate the allosteric regulation of important drug targets.

Zodiac is a Molecular Modelling suite for drug design. Its features include support for haptic devices and nintendo wiimote fully undoable command list, MMFF94 implementation, POVRAY output.

ccwatcher monitors the progress of computational chemistry calculations during runtime. It has both a GUI and a "Command Line Interface" to which it parses important output and plots SCF energies.

PAScual is a data analysis suite for Positron Annihilation Lifetime Spectroscopy (PALS).

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

3DMolvis is a tool designed to make easy learning of basic structure and function of biological molecules.

Project for develop force fields with using ab-initio calculations