Cellware

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Cellware has been designed to conduct modeling and simulation of gene regulatory and metabolic pathways and also offer an integrated environment for diverse mathematical representations, parameter estimation and optimization. In addition, a user-friendly

http://www.bii.a-star.edu.sg/research/sbg/cellware/

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2007-01-27, 10🔥, 0💬

CytoScape
Cytoscape is a visualization platform for use with molecular interaction networks. Interaction data can be integrated with other state data such as gene expression profiles. The input to Cytoscape includes lists of interaction pairs, and tab/space delimit 2007-01-27, ≈10🔥, 0💬

Swiss-PdbViewer
TraX (Trajectory eXplorer) is a simple Biodesigner-like program working under Linux and Windows. The program allows reading a protein folding simulation trajectory (TRA file) and saving a single frame as a PDB file. 2007-01-26, ≈10🔥, 0💬

Swiss-PdbViewer
Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant 2007-01-26, ≈10🔥, 0💬

E-Cell 3
E-Cell Project is an international research project aiming to model and reconstruct biological phenomena in silico, and developing necessary theoretical supports, technologies and software platforms to allow precise whole cell simulation. 2007-01-27, ≈10🔥, 0💬

VEGA
VEGA was originally developed to create a bridge between most of the molecular software packages only, but in the years, enhancing its features, it's evolved to a complete molecular modeling suite. 2007-01-26, ≈10🔥, 0💬

Gepasi
Gepasi is a software package for modeling biochemical systems. It simulates the kinetics of systems of biochemical reactions and provides a number of tools to fit models to data, optimize any function of the model, perform metabolic control analysis and l 2007-01-27, ≈10🔥, 0💬

ADVICE
Automated Detection and Validation of Interaction by Co-Evolution (ADVICE) takes a list of protein sequences or sequence pairs as input and uses orthologous sequences to assess the similarity in the evolutionary history of the proteins. It is suggested th 2007-01-27, ≈10🔥, 0💬

Reduce
Reduce is a program for adding hydrogens to a Protein Data Bank (PDB) molecular structure file. Hydrogens are added in standardized geometry with optimization of the orientations of OH, SH, NH3+, Met methyls, Asn and Gln sidechain amides, and His rings. B 2007-01-26, ∼9941🔥, 0💬

ANTHEPROT
ANTHEPROT (ANalyse THE PROTeins) is to integrate into a single package most of the methods designed for protein sequence analysis. 2007-01-27, ∼9716🔥, 0💬

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