Search Results for "surface"

WavePacket is a program package for numerical simulation of quantum-mechanical wavepacket dynamics of distinguishable particles. It can be used to solve single or coupled time-independent or time-dependent (linear) Schrödinger and Liouville-von Neumann-equations, partly also classical or quantum-classical Liouville equations. Optionally accounting for the interaction with external electric fields within the semiclassical dipole approximation, WavePacket can be used to simulate modern...

Although protein-protein interaction networks are an ubiquitous component of modern systems biology, comparatively few efforts have been made to tailor their topology to the actual cellular condition under study. Since a simple reduction of the networks to the subset of expressed genes only scratches the surface of higher organisms’ regulatory capabilities, we propose the advanced method PPIXpress that allows to exploit expression data at the transcript-level and is thus able to also reveal alterations in protein connectivity caused by alternative splicing. The original publication can be found on https://bioinformatics.oxfordjournals.org/content/32/4/571 .

The software can be used to co-localize spots in 2 or 3 movies containing single molecule fluorescence data with surface immobilized molecules. If movies are taken on more than 1 camera, offset files can be made and then used to warp one of the movies (or two of the movies if working with three). Time traces for identified spot triples and pairs can be subsequently viewed. The software was created at the University of Colorado Boulder by James Goodrich, with the help of Abigail Horn and Jennifer Kugel.

ProtPOS is a self-contained, lightweight, and easy-to-use software package for predicting the preferred orientation of protein on a given surface upon initial adsorption. It searches quickly for the low energy protein poses in all translational and rotational degrees of freedom of the protein with respect to the surface using particle swarm optimization. Each successful run returns the lowest energy orientation of the protein on the surface in PDB format, which is readily used for MD simulations. ...

This software searches the potential energy surface of small to medium size atomic systems for global minima using quantum ab initio techniques. It performs bond rotations and molecule translations and rotations on a Linux cluster with MPI.

NanoTrackJ moved to GitHub! Please see: https://github.com/thorstenwagner/ij-nanotrackj or http://fiji.sc/NanoTrackJ

Software to identify cavities and crevices in proteins. The goal is to be able to take a protein structure, and to differentiate between five different types of environments for each residue: buried, surface, interfacial, cavity, or crevice.

From a pdb file, the java program calculates the van der Walls surface of the protein in the file.

FGH is program that solves vibrational Schroedinger equation using the Fourier grid hamiltonian method. The program requires potential energy surface and G-matrix defined at the uniform grid of points.