121 projects tagged "Chemistry"

No download Website Updated 24 Feb 2007 APBS

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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 24 Feb 2007 PDB2PQR

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Pop 13.42
Vit 51.48

PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include adding a limited number of missing heavy atoms to biomolecular structures, determining side-chain pKas, placing missing hydrogens, optimizing the protein for favorable hydrogen bonding, assigning charge and radius parameters from a variety of force fields.

No download Website Updated 08 Apr 2007 PyVib2

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Pop 16.43
Vit 1.00

PyVib2 permits the automatic correlation of vibrational motions of molecules, thereby allowing an understanding of Raman, Raman optical activity (ROA), infrared vibrational absorption (IR), and vibrational circular dichroism (VCD) spectra. The versatile representation of vibrational motions, the visualization techniques of Raman/ROA and IR/VCD generation in molecules, and the production of publication quality spectra are features of PyVib2. Output files of Raman/ROA and IR/VCD calculations, produced with the DALTON and Gaussian quantum chemistry packages, can be directly opened. Files in the MOLDEN and XMol XYZ format can be imported and exported. A variety of formats (JPEG, TIFF, PNG, PNM, PS, PDF, animated GIF, and FLI) are available to the user for saving results. All the functionality is accessible via the pyviblib class library.

No download Website Updated 11 May 2007 SpectraScan

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Pop 20.20
Vit 1.00

SpectraScan loads images from scanned curves and exports the pixel coordinates of the curve in CSV format. It was designed especially for scans of ESR or other spectra, which are to be converted into a computer readable format.

Download Website Updated 07 Feb 2014 Avogadro

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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.

Download Website Updated 26 Dec 2012 massXpert mass spectrometry package

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Pop 207.70
Vit 16.07

The massXpert software package is a mass spectrometry environment for linear (bio-)polymers. It inherits all the innovations of GNU polyxmass. It allows the detailed definition of new polymer chemistries in the XpertDef module. These chemistry definitions are then used in the desktop calculator-like mass calculator (XpertCalc) and in the sophisticated polymer sequence editor and (bio-)chemical/mass spectrometric simulations module (XpertEdit). Available simulations include polymer and monomer chemical modifications, polymer sequence cleavage, gas-phase fragmentation, m/z ratio calculations, and more.

Download Website Updated 26 Jul 2007 AGM Build

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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 20 Sep 2007 Powua Client

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Pop 22.98
Vit 1.00

Powua is a parallel super-computer consisting of many processors that work simultaneously. The Powua client lets users access this high computing power from wherever they are, directly on their computer, through a simple Internet connection. If your preferred software is supported, you can start using it immediately in Powua and speed up all those processes that would otherwise occupy your processor for a long time. Powua subdivides your operation and distributes it to many processors simultaneously.

No download Website Updated 29 Feb 2008 iloog

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Pop 30.46
Vit 1.45

iloog is a Gentoo-based live CD targeted mainly at students and scientists. It features UnionFS filesystem support that enables you to write everywhere on the LiveCD and install extra packages, a graphical X environment through the Fluxbox window manager, many programming editors and IDEs, and a plethora of scientific applications, including Octave, Namd, Merlin, and full (La)TeX support.

No download Website Updated 21 Nov 2007 BioMAJ

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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.

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openAviToGif

A video to GIF converter.

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libcap-ng

An alternate POSIX capabilities library.