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         Molecular Science
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162 projects in result set. Projects sorted by: Ranking (Top Ranked First)
Select a page:   1   2   3   4   Next


1. ABFF - Project for develop force fields with using ab-initio calculations

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2. Agent-Based Multiscale Tissue Model - Agent-based multiscale model of cancer proliferation dynamics

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3. aisconvert - Toolkit for processing genetic data in RAW (23andme) format. Currently supports (command-line): Half-IBD (Identity by descent) aka HIRs - between 2 or any number of files (in distances and cM); RAW2PED conversion; regions of homozygousity

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4. AMORSS: redox enzymes simulation system - 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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5. APBS - APBS is a software package for the numerical solution of the Poisson-Boltzmann equation, a popular continuum model for describing electrostatic interactions between molecular solutes over a wide range of length scales. <http://apbs.sf.net/>.

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6. arrayplex - ArrayPlex integrates various forms of microarray data from diverse annotation and primary data sources. It provides a programmatic framework (API set) for collaborative development and deploys as easy to maintain client-server architecture.

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7. Ascalaph Graphics - Molecular Dynamics and Molecular Graphics program. Molecular model builder. Interface with the MDynaMix http://www.mmk.su.se/~sasha/mdynamix/

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8. Ascalaph Quantum - is a graphic interface and models builder for the quantum mechanics packages NWChem, CP2K and PC GAMESS/Firefly.

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9. Atomic-Clusters - This project is intended to perform Monte-Carlo-Simulations to calculate small clusters (2 to 13 atoms) of the rare gas "argon".

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10. AutoDock Software in Parallel with GPUs - Using the CUDA API this project modifies the AutoDock software to run in parallel on NVIDIA GPUs. Users will be able to download and compile the code and use AutoDock on CUDA capable Graphics Cards. Autodock is located at http://autodock.scripps.edu/

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

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12. BASILISK - BASILISK is a model of side chain conformational space in proteins. Unlike rotamer libraries, does BASILISK model the chi angles in continuous space. Furthermore features BASILISK an also continuous backbone dependence.

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13. Bio-SPICE - Our goal is to create an open source framework and toolset for modeling dynamic cellular network functions, and to develop a user community committed to using, extending and exploiting these tools to further our knowledge of biologic processes.

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14. Bioclipse - An open source workbench for chemo- and bioinformatics built on the Eclipse Rich Client Platform (RCP).

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15. Bioinformatics Template Library - The original Bioinformatics Template Library (BTL) uses templates to implement generic programming in same way as the Standard Template Library (STL). Biolib aims at continue developing this library.

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16. Biological Network Analyzer - Workbench for visualizing biological networks (regulatory, interaction, and metabolic). Can be used as a front-end for BN++ databases, but also as stand-alone tool.

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17. Biomolecule Toolkit - The Biomolecule Toolkit is a library for modeling biological macromolecules such as proteins, DNA and RNA. It provides a C++ interface for common tasks in structural biology to facilitate the development of molecular modeling, design and analysis tools.

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18. BioNLP UIMA Component Repository - The BioNLP UIMA Component Repository provides UIMA wrappers for novel and well-known 3rd-party NLP tools used in biomedical text prosessing, such as tokenizers, parsers, named entity taggers, and tools for evaluation.

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19. BioSpring - BioSpring is a molecular simulation software based on spring network model, including non-bonded interactions, especially designed for Interactive Molecular Dynamics.

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20. Bowtie - Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.

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21. bruread - bruread is a program to read and display NMR data in the Bruker XWIN-NMR format. The program has a command-line interface and a graphic display based on gnuplot. - Note that this is only an NMR spectrum *viewer*, not a full-fledged data evaluation suite

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22. Burrow-owl - Burrow-owl is a software package for visualizing multidimensional nuclear magnetic resonance (NMR) spectra, with an emphasis on spectra used in macromolecular structure determination.

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23. CAIROTEP - ORTEP-III with CAIRO graphics backend

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24. Camaro - Camaro manages cDNA and RNAi screens and their resulting datasets, detects and visualizes common artifacts, and analyzes the data in the context of a single screen or in a control-treatment configuration of several screens.

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25. cca-forum - Cca-forum unifies the Common Component Architecture tools and tutorial. It includes the CCA specifications, the Ccaffeine framework for HPC, and related tools. These support multilanguage scientific and parallel computing.

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26. CDKTools - The Octet-CDK interoperability package.

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27. Cellogica - Cellogica is a cellular logic analysis tool. It incorporates sequential logic and finite state machine to elucidate the relationship between transcription factors and corresponding gene expression.

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28. Chemical Descriptors Library (CDL) - CDL provides a generic C++ framework to write algorithms for the calculation of molecular descriptors. CDL provides efficient substructure search, fingerprints and pharmacophore algorithms, and many more for the calculation molecular descriptors.

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29. Chemical Structures - The Chemical Structures Project is a set of 3D structures of molecules in CML format. Each file contains also some physical properties, which can be access using a web browser or a CML file reader.

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30. ChIPOTle 2.0 Peak Discrimination Tool - ChIPOTle 2.0 is a user friendly tool for performing peak detection in ChIP-chip signal. The tool also has functions for probe sorting, signal normalization, replication merging, and multiple correction testing in a windows interface or *nix command line.

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31. cnsFace - cnsFace is a GUI for the Crystallography and NMR System.

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32. CoCOOT - CoCOOT is an extended collaboration system of COOT(Crystallographic Object Oriendted Toolit). It operates an add-on of original Coot. It enables to collaboration through internet.

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33. Collaborative Genome Annotation - A platform for Web-Based Collaborative Genome Annotation.

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34. Colloids - A C++ library to process both experimental and simulation data of colloidal particles. Includes a tracker (Crocker&Girer) in 2D and 3D (+time), a Leica file reader, Steindhard bond orientational order calculation, etc.

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35. CoMPAS Pro - Comprehensive Meta Prediction and Annotation Services for Proteins: The new all-in-one prediction tool that can be easily extended to include any SOAP/WSDL-enabled prediction servers. A concise user interface lets you use the results instantly.

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36. Cryo-EM Segmentation and Registration - Software for segmentation and registration of 3D density maps obtained using cryo-electron microscopy.

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37. Crystalbuilder - An easy way for single crystal structure analysis. Graphical software for single crystal structure refinement. CRYSTALBUILDER uses SHELXL-97 software for the refinement and makes directly possible the molecular structure visualization.

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38. DIY Genomics - DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV

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39. DNA Ninja - A Smooth DNA Editor - DNA Ninja will be designed as a DNA editor allowing to modify DNA files, annotate features, make restriction maps and virtual gels, pick primers and find ORFs. The main goal is that the program is intuitive to use and runs fast.

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40. DNAStrider - Mac upgraded to OSX, Lepard which do not support os9 anymore. This project is build to help DNA Strider user to get their data out and perform some basic DNA analyze function.

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41. DRCS - DRCS (Dimensionless Reaction Coordinate Software) calculates a dimensionless reaction coordinate for chemical reactions that can be used to classify transition states (and other geometries along a reaction path) as either early or late.

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42. ED Software - ED Software project contains several programs used (mostly) for processing gas-phase electron diffraction (GED) experimental data.

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43. esra - Esra is a 100% pure java library for the interactive analysis of molecular mechanics data. Mangles your data in your favorite scripting language.

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44. EYPID_PROJECT - A logical model to describe and encode protein-protein interaction data into a machine-readable format. The model (in UML) must contain information about the state of the interactiong proteins before and after the interaction for pathways building.

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45. FAUNUS: A Molecular Simulation Framework - FAUNUS is an object oriented class library for molecular simulation, written in C++/STL. It contains routines and utility programs for, Metropolis Monte Carlo sampling, Macromolecules, Proton Titration, Widom Analysis, POVRAY Visualization etc.

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46. Force - FORce based Cluster Editing (FORCE) is a Java software heuristically solving the graph cluster editing problem on weighted edges using BLAST E-values. It further provides a training mode for heuristic parameter estimation.

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47. Force Field X - FFX is a molecular biophysics tool written in pure Java. We have implemented the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field with special features for crystallography.

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48. Frankenstein Project: Hack the Genome - Frankenstein Project: Hack the Genome A collection of valuable tools needed for genome analysis, such as: - molecule, protein 3d structure viewer - protein alignement machine - cloner - DNA manipulating tools - DNA-to-Protein translator and more

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49. FuncNet - Client tools for the FuncNet protein function analysis platform: http://funcnet.eu/

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50. Gabedit - Gabedit is a Graphical User Interface for Gamess-US, Gaussian, Molcas, Molpro, MPQC, OpenMopac, Orca, PC Gamess and Q-Chem computational chemistry packages.

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162 projects in result set. Projects sorted by: Ranking (Top Ranked First)
Select a page:   1   2   3   4   Next

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