Software Updates

CcpNmr Analysis

a series of programs for macromolecular NMR including AnalysisAssign, AnalysisScreen, AnalysisMetabolomics and AnalysisStructure, and with version 3, the addition CcpNmr ChemBuild.

Olex2

an easy-to-use program containing everything you need to solve, refine and finish small-molecule crystal structures using an intuitive user interface, honed over ten years of development.

CCP4

(Collaborative Computational Project, Number 4) a collection of programs and associated data and software libraries used for macromolecular structure determination by X-ray crystallography.

Blender

a 3D creation suite that supports the entirety of the 3D pipeline—modeling, rigging, animation, simulation, rendering, compositing and motion tracking.

TOMOMAN

a MATLAB package for managing the various preprocessing steps for taking raw data to reconstructed tomograms. TOMOMAN mainly acts as a set of wrapper scripts for external packages, managing the input and outputs of each external module to form a cohesive pipeline.

STOPGAP

a subtomogram averaging workflow written in MATLAB for performing a number of subtomogram averaging tasks including template matching, high-resolution alignment and averaging, and classification.

Blender

a 3D creation suite that supports the entirety of the 3D pipeline—modeling, rigging, animation, simulation, rendering, compositing and motion tracking.

MGLTools

a software package for visualization and analysis of molecular structures comprising AutoDockTools (ADT): a graphical front-end for setting up and running AutoDock; Python Molecule Viewer (PMV); and Vision: a visual-programming environment for building networks describing novel combinations of computational methods and yielding new visualizations of their data.

Schrodinger

a suite of tools for drug discovery. The Schrodinger suite runs on Linux and Mac workstations, but due to its size, it is not included in our default installation.

reliosparc

a Python Utilities program for converting between Cryosparc and Relion File Formats

Gautomatch

a GPU-accelerated program for accurate, fast, flexible and fully automatic particle picking from cryo-EM micrographs with or without templates.

DRGN-AI

a neural network-based algorithm for ab initio heterogeneous cryo-EM reconstruction.

PyMOL

a widely used molecular visualization package developed by Warren DeLano, now maintained by Schödinger, LLC. This installation includes official incentive builds of PyMOL.

DOCK

a molecular docking application used to a) predict binding modes of small molecule-protein complexes; b) search databases of ligands for compounds that inhibit enzyme activity, bind a particular protein, bind nucleic acid targets; c) examine possible binding orientations of protein-protein and protein-DNA complexes; d) help guide synthetic efforts by examining small molecules that are computationally derivatized. Dock is offered in the SBGrid collection in two iterations, Dock 3 and Dock 6.

Geneious

a powerful and comprehensive suite of molecular biology and NGS analysis tools.

AreTomo3

a multi-GPU accelerated software package that enables real-time fully automated reconstruction of cryoET tomograms in parallel with cryoET data collection.

LigPlot+

a successor to the original LIGPLOT program for automatic generation of 2D ligand-protein interaction diagrams. It is run from an intuitive java interface which allows on-screen editing of the plots via mouse click-and-drag operations.

cryoDRGN

a neural network based algorithm for heterogeneous cryo-EM reconstruction. In particular, the method models a continuous distribution over 3D structures by using a neural network based representation for the volume.

crYOLO

a novel automated particle picking software based on the deep learning object detection system 'You Only Look Once' (YOLO). CrYOLO is available as a standalone program under http://sphire.mpg.de/ and is part of the image processing workflow in SPHIRE.

cryoDRGN

a neural network based algorithm for heterogeneous cryo-EM reconstruction. In particular, the method models a continuous distribution over 3D structures by using a neural network based representation for the volume.

BioXTAS RAW

a program for analysis of SAXS data that enables creation of 1D scattering profiles from 2D detector images, standard data operations such as averaging and subtraction, analysis of radius of gyration (Rg) and molecular weight, and advanced processing using GNOM, DAMMIF, and AMBIMETER. It also allows easy processing of inline SEC-SAXS data.

Geneious

a powerful and comprehensive suite of molecular biology and NGS analysis tools.

EM-GAN

a computational tool which enables capturing protein structure information from cryo-EM maps more effectively than raw maps.

ColabDesign

a tool that makes protein design accessible through Jupyter notebooks by using advanced protein structure prediction models like AlphaFold and TrRosetta for designing novel proteins with targeted structures.

Starparser

a package implemented in Python to manipulate Relion star files including counting, modifying, plotting, and sifting the data.

CTFFIND 5

a new version of the cisTEM program CTFFIND with improved CTF estimation for cryoEM.

NAMD

a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.