Software Updates

AlphaPulldown

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

Napari-SegSelect

Plugin for Napari to select a connected component from a Membrain-seg segmentation.

Surface Morphometrics Pipeline

a pipeline of tools to generate robust open mesh surfaces from voxel segmentations of biological membranes using the Screened Poisson algorithm and calculate morphological features including curvature and membrane-membrane distance using pycurv's vector voting framework with tools to convert these morphological quantities into morphometric insights.

MPicker

a tool for membrane flatten and visualization.

SAMtools

(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.

MiCSPARC

is a CryoSPARC-based cryo-EM pipeline for microtubule image processing that combines automated filament tracing, particle picking, fast 3D refinement, protofilament-number assignment, alignment, register correction, and seam search to determine structures of decorated and undecorated microtubules. It includes Python utilities for filament extrapolation, reference generation, protofilament assignment, and angular unification, with a conda environment targeting cryosparc-tools 4.7.1. The workflow is designed for end-to-end microtubule reconstruction in CryoSPARC, from curated exposures and template generation through high-resolution protofilament and full microtubule refinement.

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.

SAMtools

(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.

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.

Doppio

a new web-based user interface for CCP-EM and RELION software.

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.

PHENIX

(Python-based Hierarchical Environment for INtegrated Xtallography) a software suite for the automated determination of molecular structures using X-ray crystallography and other methods.

OpenJDK

(Open Java Development Kit) a free and open source implementation of the Java Platform, Standard Edition (Java SE).

PXDesign

is a de novo protein-binder design suite combining a diffusion generator (PXDesign-d) with Protenix and AF2-IG confidence models for candidate selection and ranking. It supports YAML-defined target preparation, MSA-assisted extended runs, preview and generation-only modes, and output filtering with AF2-IG and Protenix success criteria to prioritize binders for wet-lab validation.

OpenFold

a trainable, memory-efficient, and GPU-friendly PyTorch reproduction of DeepMind's AlphaFold 2.

PXDesignBench

is a protein design evaluation suite for monomer and binder tasks that standardizes sequence generation, structure consistency assessment, and downstream metrics across tools including ProteinMPNN, ESMFold, AlphaFold2, and Protenix. It provides task-specific pipelines, wrappers for external models, and configurable JSON- or directory-based inputs for batch evaluation, bias-controlled ProteinMPNN sampling, and multi-GPU or distributed execution. Outputs include confidence and self-consistency metrics, designability and shape-based structural statistics, and summary CSVs for comparative analysis and post-processing.

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.

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.