Jourmore's repositories
PockDrug_descriptors
This script calculates the PockDrug descriptors of a protein pocket.
GA_for_Feature_Selection
使用遗传算法结合决策树做特征选择/Using genetic algorithm for feature selection with decision tree
pyProCT
pyProCT is an open source cluster analysis software especially adapted for jobs related with structural proteomics. Its approach allows users to define a clustering goal (clustering hypothesis) based on their domain knowledge. This hypothesis will guide the software in order to find the best algorithm and parameters (including the number of clusters) to obtain the result that fulfills their expectatives. In this way users do not need to use cluster analysis algorithms as a black box, improving this way the results. pyProCT not only generates a resulting clustering, it also implements some use cases like the extraction of representatives or trajectory redundance elimination.
SSS-Drawer
Simple python script to visualise secondary structures as a single SVG image.
dpocket_extractor
Runs dpocket to get pocket descriptors for a given set of atoms or residues
Interactive-Visualization-of-Biological-Networks
PLViz (Pathway Logic Visualization) is a web based tool for the visualization, interpretation and analysis of pathway knowledge pertaining to protein models. In this Visualization, we introduce an exploratory approach that initially provides a choate view of the entire protein model and enables the user to analyze each protein in the model by separately viewing its activation, subsequent protein activations and the interactions of the protein with other proteins in the model. The visual representation of the proteins and the interactions among them is shown using a tree structure. The visualization of this kind of structure is efficiently done using the node-link diagram. In this visualization, the proteins are shown in the form of nodes and the interaction between each pair of protein is shown using a link between the two proteins. For each element of visualization, effective color coding is applied to differentiate different types of proteins and interactions. The dataset used for this visualization includes individual descriptions of each protein as well as each interaction, thus leading to redundancy. In order to reduce redundancy, all the redundant nodes in the data are merged into one unique node in the pathway diagram. The initial global view of the model is smoothly transitioned into the protein-level view to enable further insight into the origin or interactions of a particular protein.
clusfps
A Molecular cluster tools built on RDKit
SimpleGA
用python实现简单的遗传算法
pymdlog
a tool for analyzing log files generated by molecular dynamics simulation packages
pyProCT-GUI
Javascript-based interface for pyProCT
emdy_gui
a PyMOL plugin for setting up molecular dynamics simulations