Software Updates

HADDOCK

(High Ambiguity Driven biomolecular DOCKing) relies on an approach that makes use of biochemical and/or biophysical interaction data, such as chemical shift perturbation data resulting from NMR titration experiments, mutagenesis data or bioinformatic predictions.

RStudio

an integrated development environment (IDE) for R that includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

CUDA

a tool that helps redistributable software libraries to support CUDA applications for Linux.

UNIO

a program that performs automated NMR data analysis for protein 3D structure determination. It represents the result of more than a decade of innovative research performed in order to enable accurate, objective and highly automated protein structure determination by NMR.

VinaLC

a parallel molecular docking program that is a modified version of the very popular PC-based molecular docking program AutoDock Vina. VinaLC is a message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines.

ATSAS

a program suite for small-angle scattering (SAXS) data analysis from biological macromolecules.

IMOD

a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections.

RELION

(REgularised LIkelihood OptimisatioN) a stand-alone computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.

DireX

a tool that performs efficient geometry-based conformational sampling of protein structures under experimental restraints. It combines prior structural information with experimental data through the Deformable Elastic Network (DEN) approach which drastically reduces over-fitting.

HKL2000

a data processing suite for X-ray crystallography that provides a sleek interface for devising a data collection strategy and processing data. HKL is based on the extended versions of Denzo, Xdisplayf and Scalepack. HKL was developed and is maintained by Wladek Minor (University of Virginia).

MotionCor2

a multi-GPU program that corrects beam-induced sample motion on dose fractionated movie stacks. It implements a robust iterative alignment algorithm that delivers precise measurement and correction of both global and non-uniform local motions at single pixel level across the whole frame, suitable for both single-particle and tomographic images.

CCP-EM

(Collaborative Computational Project for Electron cryo-Microscopy) a software framework and resulting software suite that includes tools for project and data management along with a focus on building and refinement of atomic models into cryo-EM reconstructions. The framework allows easy access to various programs and utilities from collaborators via Python task wrappers and a user-friendly graphical user interface or a command-line interface suitable for scripting.

Jupyter

a language-agnostic HTML notebook application for Project Jupyter.

Theseus

a program for the simultaneous superpositioning and analysis of multiple macromolecular structures via the method of maximum likelihood (ML).