Software Updates

RDKit

a collection of cheminformatics and machine-learning software written in C++ and Python.

Gen-COMPAS

is a generative committor-guided path sampling framework for studying rare events such as protein conformational changes. It combines diffusion models that generate new protein structures with Variational Committor Networks that learn reaction coordinates, then automates targeted and unbiased NAMD simulations, RiteWeight trajectory reweighting, and free-energy landscape estimation in an iterative, restartable workflow with a GUI helper for building configuration files.

RobPicker

is a particle picker for cryo-electron tomography that makes supervised picking more robust to noisy or imperfect training labels. RobPicker allows users to train models on their own tomograms in MRC format with particle coordinates converted from STAR files, and provides command-line tools for training, threshold selection, and picking particles in new tomograms.

cryoPARES

uses supervised deep learning to assign poses to cryo-EM particles, training a model on a RELION-aligned dataset and reusing it to align new datasets of the same or closely related molecules, such as ligand screening series. It includes local refinement by projection matching, 3D reconstruction, B-factor sharpening, and a daemon mode for processing particles during data collection.

MemBrain-Seg

a tool for membrane segmentation in 3D for cryo-electron tomography (cryo-ET).

DIALS

(Diffraction Integration for Advanced Light Sources) a software project for the analysis of crystallographic diffraction images for many new methods from shutterless, fine-sliced rotation scans to randomly-oriented snapshots of serial crystallography. It uses multiple CPU and GPU machines to increase speed and accuracy based on a comprehensive physical model.

AreTomo3

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

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.

PowerFit

a Python package and simple command-line program to automatically fit high-resolution atomic structures in cryo-EM densities.

AlphaJudge

is a Python pipeline for evaluating AlphaFold2 and AlphaFold3 protein complex predictions by combining model confidence metrics such as ipTM, pTM, pLDDT, and PAE with interface-level biophysical descriptors including contacts, hydrogen bonds, salt bridges, buried area, solvation proxy, and shape complementarity.

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.

AmberTools

a suite of programs that allows users to carry out molecular dynamics simulations, particularly on biomolecules. The suite can be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB) with either explicit water or generalized Born solvent models. The independently developed packages work well by themselves, and with Amber itself.

Surface Morphometrics GUI

is a graphical interface for quantifying membrane ultrastructure in cryo-electron tomography data. It supports generating surface meshes from segmentations, measuring membrane curvature, distances, and relative orientations, and interactively visualizing the results in 3D.

Pom

a tool for scaling data analyses in cellular cryoET using comprehensive segmentation.

DeepRank-GNN-esm

a graph neural network framework for scoring protein-protein interfaces that incorporates ESM-2 language model embeddings. The tool provides both a command-line interface for direct complex scoring and a Python framework for custom applications, generating predictions of interface quality (fnat values) from PDB structures. It includes pre-trained models and supports both CPU and GPU environments for analyzing protein-protein binding interfaces.

AlphaJudge

is a Python pipeline for evaluating AlphaFold2 and AlphaFold3 protein complex predictions by combining model confidence metrics such as ipTM, pTM, pLDDT, and PAE with interface-level biophysical descriptors including contacts, hydrogen bonds, salt bridges, buried area, solvation proxy, and shape complementarity.

Ais

a tool that provides annotation and segmentation of cryo-ET data using convolutional neural networks.

AlphaFold3

predicts 3D molecular structures and their interactions. It generalizes the original "protein‑only" AlphaFold into a model for whole biomolecular complexes, including proteins, DNA, RNA, and ligands (small molecules).

CCPEM-pipeliner

an integrated suite of software tools for processing single particle cryoEM data, from preprocessing raw image data through building and fitting atomic models.