JabberDock tackles the problem of protein-protein docking while accommodating for rearrangements upon binding including side chain reorientations and backbone flexibility.
ADAM (Analysis of Dynamic Algebraic Models) uses a combination of simulation and mathematical algorithms to analyze the dynamics of discrete biological systems.
SimBoolNet is an open source Cytoscape plugin that simulates the dynamics of signaling transduction using Boolean networks. Given a user-specified level of stimulation to signal receptors, SimBoolNet simulates the response of downstream molecules and visualizes with animation and records the dynamic changes of the network.
MOLARIS-XG includes powerful programs POLARIS and ENZYMIX in a unique package with an extremely improved interface and maximum robustness. MOLARIS incorporates the methodologies of the old packages ENZYMIX and POLARIS and also the more recent advances developed in our group:
ENZYMIX is a macromolecular simulation program designed to study the functions of proteins ranging from ligand binding to free energy profiles of enzymatic reactions using the Empirical Valence Bond (EVB) approach and the Free Energy Perturbation (FEP) method.
POLARIS is a fast converging computational software based on the Protein Dipoles-Langevin Dipoles (PDLD) approach, it is used for the calculation of free energies and electrostactic properties of molecules and macromolecules in solution through the evaluation of the permanent dipoles, induce dipoles, charges, dispersion contributions and hydrophobicity.
MERMAID (Martini coarsE gRained MembrAne proteIn Dynamics) is a publicly available web interface that allows the user to prepare and run coarse-grained molecular dynamics (CGMD) simulations and to analyse the trajectories
TESD simulates the number of genomic TE copies in different populations across generations (according to the Island Model), using classical models of TE dynamics. The parameters of the models (transposition and excision rates, selection intensity, recombination rate, migration rate, population sizes and number of populations) are defined by the users.
ProDy is a free and open-source Python package for analysis and modeling of protein structural dynamics. It allows for efficient analysis of large datasets and is suitable for development or prototyping of structure-based analysis and modeling software.
The program treekin computes folding dynamics on coarse grained version of an energy landscape, where all conformations belonging to the same local minimum have been contracted into a single macro-state.