Software Updates

PyMOL

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

AreTomo3

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

MemBrain-v2

MemBrain v2 includes MemBrain-seg, MemBrain-pick, MemBrain-stats, and several Napari tools.

AFMassive

is a modified AlphaFold implementation for massive conformational sampling, derived from AlphaFold v2.3.2 and designed to integrate with MassiveFold for parallelized prediction workflows.

Scipion

an image processing framework to obtain 3D models of macromolecular complexes using 3D EM that allows you to execute workflows combining different software tools, while taking care of formats and conversions.

ChimeraX

a tool of 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.

BCFtools

a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

Open Force Field Toolkit

a Python toolkit for the development and application of modern molecular mechanics force fields, leveraging direct chemical perception and rigorous statistical parameterization methods.

Xmipp

(X-Window-based Microscopy Image Processing Package) a suite of image processing programs primarily aimed at single-particle 3D electron microscopy.

OpenFreeEnergy

is a Python package for executing alchemical free energy calculations.

qFit

a collection of programs for modeling multi-conformer protein structures.

R

a free software environment for statistical computing and graphics.

qFit

a collection of programs for modeling multi-conformer protein structures.

Volume_Seg_Tool

a tool that utilizes deep learning to perform volumetric electron microscopy image segmentations, both semantic and instance segmentation.

MassiveFold

is a tool designed to expand structure prediction sampling by optimizing the parallelization of AlphaFold-based predictions across GPU clusters.

MolDiff

is a diffusion framework designed for generating 3D drug-like molecules, achieving a sampling success rate of over 99%. This tool addresses the atom-bond inconsistency problem in 3D molecule diffusion generation and serves as a backbone for applications such as pocket-based generation and linker generation.

GAPSTOP(TM)

is GPU-Accelerated Python STOPgap for Template Matching for fast template matching (TM) in cryo electron tomograms that is based on TM routines from STOPGAP.

MolSnapper

is a tool for conditioning diffusion models to generate 3D drug-like molecules, built on the MolDiff codebase. It integrates pretrained models and provides a streamlined workflow for sampling molecules from defined pockets, making it suitable for structure-based drug design applications.

protein-quest

is a Python package to search/retrieve/filter proteins and protein structures.

Coot

(Crystallographic Object-Oriented Toolkit) an application that supports model building and real space refinement. This application interfaces with refmac, Phenix, and several other applications. Coot was recognized as the best structural biology application in 2008 by SBGrid.

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.