Software Updates

GWOVina

Protein-ligand docking programs are indispensable tools for predicting the binding pose of a ligand to the receptor protein. Based on the implementation of AutoDock Vina, GWOVina employs grey wolf optimization (GWO) algorithm to speed up the search for optimal ligand poses.

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.

pyemma

a Python library for the estimation, validation and analysis Markov models of molecular kinetics and other kinetic and thermodynamic models from molecular dynamics (MD) data.

CTFFIND 4

a new version of ctffind (a program for finding CTFs of electron micrographs) that should run significantly faster than CTFFIND 3 and may give slightly improved results when processing data from detectors other than scanned photographic film.

DataWarrior

an Open-Source Program for Data Visualization and Analysis with Chemical Intelligence

GROMACS

a versatile package that performs molecular dynamics of proteins, lipids and nucleic acids.

ChimeraX

the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. Compared to Chimera, ChimeraX has improved graphics (e.g. interactive ambient shadows); faster handling of large structures (millions of atoms); and a more modern, single-window user interface.

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.

CUDA

redistributable software libraries to support CUDA applications for Linux.

MDTraj

A modern, open library for the analysis of molecular dynamics trajectories

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.

CUDA

redistributable software libraries to support CUDA applications for Linux.

ModelAngelo

an automatic atomic model building program for cryo-EM maps.

PyMOL

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

SRA Toolkit

(Sequence Read Archive Toolkit) a collection of tools and libraries for using data in the INSDC Sequence Read Archives.

mcm-cryoet

Mean curvature motion and levelset motion for cryo-ET

TomoTwin-cryoet

a deep metric learning based particle picking procedure for cryo-ET

AlphaPulldown

a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer.

PyMOL (Schrodinger)

PyMOL from Schrodinger LLC

CellProfiler

is a cell image analysis software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

Careless

merges crystallography data without much physics. It performs scaling, merging, and French-Wilson corrections in a single step by directly inferring structure factor amplitudes from unscaled, unmerged intensities.

PyMOL (Schrodinger)

PyMOL from Schrodinger LLC

PyMOL

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

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.

CellProfiler

is a cell image analysis software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

bedtools

a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic. Bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

ChimeraX

the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. Compared to Chimera, ChimeraX has improved graphics (e.g. interactive ambient shadows); faster handling of large structures (millions of atoms); and a more modern, single-window user interface.

VMD

a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

Python

a general-purpose, interpreted, object oriented, high-level dynamic programming language that emphasizes code readability. Its syntax allows programmers to express concepts in fewer lines of code than in C++ or Java, thus allowing programmers to work more quickly and integrate their systems more effectively.

ChimeraX

the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. Compared to Chimera, ChimeraX has improved graphics (e.g. interactive ambient shadows); faster handling of large structures (millions of atoms); and a more modern, single-window user interface.

Chimera

a highly extensible, interactive molecular graphics program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. It is often a tool of choice for rendering EM volumes.

PyHI

a Python-based GUI program for indexing power spectra of helical assemblies.