121 projects tagged "Chemistry"

Download Website Updated 26 Jul 2007 AGM Build

Screenshot
Pop 22.49
Vit 49.98

AGM Build is a molecular builder and conformational editor. It can be used for interactive model preparation for molecular dynamics simulations, including association of atom types and partial charges. It features geometry editing, lattice building, building of chain molecules (e.g. proteins), chains with predetermined conformations, and charges and atom types according to selected Force Field.

No download Website Updated 24 Feb 2007 APBS

Screenshot
Pop 23.62
Vit 51.48

APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, and biomolecular titration studies.

No download Website Updated 22 Mar 2010 Ascalaph

Screenshot
Pop 21.31
Vit 39.11

Ascalaph is a general purpose 3D graphical molecular modeling suite that performs molecular mechanics and molecular dynamics simulations as well as quantum mechanics calculations.

No download Website Updated 16 Apr 2004 Asymptopia Flashcard System

Screenshot
Pop 50.20
Vit 3.26

Asymptopia Flashcard System uses Motif and LaTeX to produce, manage, and use attractively formatted flashcards. You load some or all of your "collections" and set the timer for pop-up frequency. The GUI interface and "Collection Manager" make creating and modifying flashcards as simple as pushing a single button. A knowledge of LaTeX is only required when entering special symbols.

Download Website Updated 07 Feb 2014 Avogadro

Screenshot
Pop 91.44
Vit 3.26

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

No download Website Updated 07 Dec 2010 BALL

Screenshot
Pop 141.95
Vit 3.53

The Biochemical ALgorithms Library (BALL) is a framework for rapid application development in molecular modeling and structural bioinformatics. BALL provides an extensive set of data structures as well as classes for molecular mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, NMR shift prediction, and visualization. Its extensibility results from an object-oriented and generic programming approach.

Download Website Updated 28 Oct 2011 BALLView

Screenshot
Pop 61.25
Vit 6.59

BALLView is an extensible viewer for bio-molecular structures. It provides all standard models and offers rich functionality for molecular modeling and simulation, including molecular mechanics methods (AMBER, CHARMM, and MMFF94 force fields), continuum electrostatics methods employing a Finite-Difference Poisson Boltzmann solver, secondary structure calculation, molecular editing and docking. Since BALLView is based on BALL (the Biochemical ALgorithms Library), it is easily extensible on the level of C++ code. In addition, it provides a Python interface with Integrated Development Environment features to allow interactive rapid prototyping.

Download Website Updated 07 Jan 2010 BKChem

Screenshot
Pop 89.08
Vit 12.44

BKChem is a chemical drawing program.

Download Website Updated 15 Mar 2002 BioJava

Screenshot
Pop 150.45
Vit 2.38

BioJava aims to provide a comprehensive set of Java components for the rapid development of applications in Bioinformatics. It contains interfaces for representing Sequences, Features, and other important bioinformatics concepts. It can also read and write sequence data in a variety of common formats and communicate with Ensembl databases and with DAS and BioCorba servers.

No download Website Updated 21 Nov 2007 BioMAJ

Screenshot
Pop 22.18
Vit 1.00

BioMAJ (BIOlogie Mises A Jour) is a workflow engine dedicated to data synchronization and processing. It automates the update cycle and the supervision of the locally mirrored data repository. The application is generalist, but was applied in the bioinformatics field for biological data bank management. The packaging includes workflow and indexing post-processing scripts for most used biological data banks. Developed in Java and Ant, the application is compatible with various Unix-based systems.

Screenshot

Project Spotlight

openAviToGif

A video to GIF converter.

Screenshot

Project Spotlight

libcap-ng

An alternate POSIX capabilities library.