We are proud to introduce version 3 of CAMPARI. This is a big step from version 2 primarily due to the comprehensive OpenMP (threads parallelism) support and due to significant improvements in both usability and performance. We have also again added a number of new algorithms from the recent literature, and CAMPARI of course continues […]
An ensemble of mathematical model is presented that all show diauxic growth behaviour of a bacterial culture. Carbon catabolite repression (CCR) is the main mechanism controlling carbohydrate uptake in bacteria, and therefore also controlling whether or not different carbon sources are metabolized in parallel or sequentially. Although described as a paradigm of the regulation of […]
This is a collection of software modifications created to integrate NanoEngineer-1, PACKMOL and MSI2LMP for the purpose of easily creating molecular dynamics cells. NanoEngineer-1 is a molecular CAD software written by Nanorex and provides the user an easy way to create molecules, while the software modifications allow the user to type atoms using multiple force […]
ParticleVis is a visualization tool specialized for loading and exploring particulate simulation data. It contains a set of features that enables powerful and useful visualizations of particle simulations to be quickly generated. Support is provided for visualization of hundreds of thousands of particles on commodity workstations, using OpenGL. Functionality includes data exploration, debugging of simulation […]
This python package aims to help people set up and analyze molecular dynamics simulations in aqueous-organic solvent mixtures. See D. Alvarez-Garcia et al. Journal of Medicinal Chemistry, 2014. If you are like the rest of our user community, your IT team is busy. With pressure to deliver on-time projects, you don’t have a lot of […]
Molecular Graphics, Molecular Dynamics, Optimization, Quantum chemistry. Molecular model building. Explicit and implicit water models. http://www.biomolecular-modeling.com/Products.html You’re probably paying too much for cell phone service. Wirefly compares hundreds of plans to help you save. Enter what you need (minutes, data, texts) into Wirefly’s innovative plan comparison tools and see your savings instantly.
An open-source software to convert SDF files into TINKER XYZ files (and viceversa) with automatic assignment of MMFF94 atom types, bond types and charges You’re probably paying too much for cell phone service. Wirefly compares hundreds of plans to help you save. Enter what you need (minutes, data, texts) into Wirefly’s innovative plan comparison tools […]
MEMBPLUGIN is a membrane analysis tool for molecular-dynamics simulations. It is a collection of visual and command-line tools that can be run within the Visual Molecular Dynamics (VMD) environment to analyze biomolecular simulations of lipid bilayers. If you are like the rest of our user community, your IT team is busy. With pressure to deliver […]
xPyder is a PyMOL plugin to analyze and visualize on the 3D structure dynamical cross-correlation matrices (DCCM), linear mutual information (LMI), communication propensities (CP), intra- and inter-molecular interactions (e.g. PSN), and more, to produce highly customizable publication-quality images. xPyder identifies networks (using concepts from graph theory, such as hubs and shortest path searching), compares matrices […]
We here present a novel computer algorithm, called AutoClickChem, capable of performing many click-chemistry reactions in silico. In silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization. Today’s small-to-medium-sized (SMB) businesses and large enterprises are saving on their monthly communications costs by making one simple decision: to switch to […]