Actively Supported Software and Web Services

OMPL: The Open Motion Planning Library

OMPL is a lightweight, thread-safe, easy to use, and extensible library for sampling-based motion planning. The code is written in C++, includes Python bindings and is released under the BSD license. OMPL is also integrated with ROS. On top of the OMPL library, we have developed OMPL.app: a GUI for rigid body motion planning that allows users to load a variety of mesh formats that define a robot and its environment, define start and goal states, and play around with different planners.

DINC

DINC is a parallelized meta-docking method for the incremental docking of large ligands (currently using AutoDock Vina)

APE-Gen: Anchored Peptide-MHC Ensemble Generator

APE-Gen is a fast method for generating ensembles of bound pMHC conformations. It generates an ensemble of bound conformations by iterated rounds of (i) anchoring the ends of a given peptide near known pockets in the binding site of the MHC, (ii) sampling peptide backbone conformations with loop modelling, and then (iii) performing energy minimization to fix steric clashes, accumulating conformations at each round.

TMKit

The Task-Motion Kit (TMKit) is a framework for Task and Motion Planning. Everyday activities, e.g., setting a table or making coffee, combine discrete decisions about objects and actions with geometric decisions about collision free motion. TMKit jointly reasons about task-level objectives, i.e., choosing actions and objects, and motion-level objectives, i.e., finding collision free paths.

Metabolite Translator

Metabolite Translator predicts human metabolites for small molecules including drugs. It is build upon a Neural Machine Translation algorithm representing molecules as sequences using the SMILES notation. Metabolite Translator converts the SMILES of the initial molecule into the SMILES representations of the metabolites that can be possibly formed in the human body. The method has been trained on data that cover metabolism of xenobiotics as well as endogenous compounds and therefore it can predict metabolites through a wide range of enzymes including the enzymes of phase I and phase II drug metabolism.

Metabolic Pathfinding Using Atom Tracking

A web server for finding metabolic pathways by using atom tracking. (Private use)

LabelHash: A Server for Matching Structural Protein Motifs

A web server for matching 3D structural motifs in proteins against the proteins in the Protein Data Bank. With a plugin for Chimera the match results can be visualized.

FASST Live

FASST Live is a web server for identifying clusters of proteins that share local structural similarity. (Private use)

OOPSMP: An Object-Oriented Programming System for Motion Planning

OOPSMP is a package for motion planning that is easy to extend, robust, and efficient. It can be used for motion planning research or as a teaching tool. This package is still available for download, but is no longer further developed (except for minor bug fixes).

RACOGS: Reconstruction Algorithm for COarse-Grain Structures

A web server for reconstructing all-atom protein structures from coarse grain structures. (Private use)

The Rice Wireless Localization Toolkit

The Rice Wireless Localization Toolkit can be used to estimate the position of a device based on the signal strength of nearby 802.11 wireless access points. While prior systems have required significant investments of human labor to build a detailed signal map, our system can be trained by spending less than one minute per office or region, and can then localize the device with very high accuracy after only two or three signal strength measurements.