Projects tagged ‘cheminformatics’

Kalzium is an application which will show you some information about the periodic system of the elements. Therefore you could use it as an information database. It also includes an equation solver and 3D viewer for molecules.

Jmol is a Java molecular viewer for three-dimensional chemical structures. Features include reading a variety of file types and output from quantum chemistry programs, and animation of multi-frame files and computed normal modes from quantum programs.

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.

The Chemistry Development Kit (CDK) is a library of Java classes for chemo-, bioinformatics, computational chemistry, and chemometrics. It provides important algorithms like substructure search, SMILES, Gasteiger charges, QSAR descriptor calculation, 3D structure generation, 2D layout and rendering, many IO formats, atom typing, and more.

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

The Bioclipse project is aimed at creating a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). Bioclipse, as any RCP application, is based on a plugin architecture that inherits ... [More] basic functionality and visual interfaces from Eclipse, such as help system, software updates, preferences, cross-platform deployment etc. [Less]

JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.

cclib is an open source library, written in Python, for parsing and interpreting the results of computational chemistry packages. The goals of cclib are: * to facilitate the implementation of algorithms that are not specific to a particular ... [More] computational chemistry package * to provide a simple and standard interface to the results of computational chemistry calculations, particularly those results that are useful for algorithms or visualisation * to maximise interoperability with other open source computational chemistry and cheminformatic software libraries [Less]

QuteMol is an open source (GPL), interactive, high quality molecular visualization system. QuteMol exploits the current GPU capabilities through OpenGL shaders to offers an array of innovative visual effects. QuteMol visualization techniques are ... [More] aimed at improving clarity and an easier understanding of the 3D shape and structure of large molecules or complex proteins. * Real Time Ambient Occlusion * Depth Aware Silhouette Enhancement * Ball and Sticks, Space-Fill and Liquorice visualization modes * High resolution antialiased snapshots for creating publication quality renderings * Automatic generation of animated gifs of rotating molecules for web pages animations * Interactive rendering of large molecules and protein (>100k atoms) * Standard PDB input [Less]

The Internet has brought together a group of chemists/programmers/informaticians who are driven by wanting to do things better, but are frustrated with the Closed systems that chemists currently have to work with. They share a belief in the concepts ... [More] of Open Source, Open Standards and Open Data (but not necessarily Open Access). And they express this in code, data, algorithms, specifications, tutorials, demonstrations, articles and anything that helps get the message across. [Less]

JaCuda is a small project which provides several mathematical function useful for a chemist or somebody working with mass specs. These functions will be executed using a cuda compatible gpu or if none is available it will fall back to the c++ ... [More] implementation. If this is also not possible we will invoke the function defined in the programming language. Which would be java/groovy for now and later python. --this project is abounded for the benefit of pycuda-- [Less]

The BinBase Database system was created to provide an accurate and fast solution for the analysis of thousand of Chromatograms and to create a library of compounds. Better known as Bins. The system is so designed that it can be easily extended and ... [More] adapted for your specific problems. You also have the possibilities to use it in different runtime configurations like: * using it as standalone system * using it with a cluster * using it with setupX as meta information provider * using with a custom meta information provider BinBase core part is now available in the svn. Websites are down to server error and we are working on it! [Less]

A collection of cheminformatics and machine-learning software written in C++ and Python.

Mistakes are the portals of discovery. James Joyce (1882-1941) A metabolic network is defined as the set of biochemical reactions that the enzymes coded for in an organism's genome are capable of catalyzing. When the network of an organism is ... [More] derived from pathway databases, it needs to be debugged for incoherences e.g., the metabolic model must obey mass balance laws. incompleteness e.g., the metabolic model is missing known reactions, genes, or compounds inconsistencies e.g., The metabolic model is inconsistent with experimental results Because of these issues, reconstructing metabolic networks from annotated genomes is currently a time-consuming, error-prone process. We develop BioHacker, a debugger for metabolic networks. BioHacker not only detects these issues, but also generates explanations as to where the problems lie and generates hypotheses for how to fix them. Read the BioHacker paper (PDF). Check out the source code. [Less]

molsKetch is a molecular drawing tool for 2D molecular structures. Its goal is to help you draw molecules quick and easily. Of course you're creation can be exported afterwards in high quality in a number of vector and bitmap formats.

Estimates toxic hazard of chemical compounds based on a decision tree approach. Provides a plugin framework to incorporate different approaches to the estimation. Platform independent (written in Java).

PD - Molecular Simulation Software