Software Updates

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.

AF3Complex

is a model equipped with the same improvements as AF2Complex, along with a novel method for excluding ligands, built on AlphaFold 3.

PocketXMol

is a pocket-interacting molecular generative foundation model for unified 3D molecular generation via learned atomic interactions. It supports structure prediction tasks such as small-molecule docking, peptide docking, and conformation generation, as well as structure-based drug design, fragment linking/growing, PROTAC design, linear and cyclic peptide design, peptide inverse folding, and partial complex prediction or generation. The release includes Conda setup files, model-weight download instructions, Colab notebooks, sampling examples, benchmarking guides, and training/data-processing documentation.

TomoNet

a software package with a modern graphical user interface to carry out the entire pipeline of cryoET and subtomogram averaging to achieve high resolution.

Pom

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

easymode

a collection of general pretrained networks for cellular cryoET.

Ais

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

Avogadro

an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.

Foldtree

a snakemake workflow for making and benchmarking structure based trees using Foldseek.

ROCKET

is a tool for refining AlphaFold predictions using crystallographic and cryo-EM likelihood targets. It integrates with OpenFold to condition experimental structure determination on pretrained neural networks, requiring both OpenFold and Phenix installations for automatic data preprocessing and post-refinement geometry polishing.

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.

OpenMM

a high performance toolkit for molecular simulation that can be used either as a stand-alone application for running simulations or as a library you call from your own code.

CCP-EM

(Collaborative Computational Project for Electron cryo-Microscopy) a software framework and resulting software suite that includes tools for project and data management along with a focus on building and refinement of atomic models into cryo-EM reconstructions. The framework allows easy access to various programs and utilities from collaborators via Python task wrappers and a user-friendly graphical user interface or a command-line interface suitable for scripting.

BioEmu

is a model that samples from the approximated equilibrium distribution of structures for a protein monomer, given its amino acid sequence.

AlphaFold

an implementation of the inference pipeline of AlphaFold using a completely new model that was entered in CASP14.

TomoNet

a software package with a modern graphical user interface to carry out the entire pipeline of cryoET and subtomogram averaging to achieve high resolution.

slabpick

is a collection of tools to facilitate particle picking and curation from 2D projections of tomography data from either slabs (projected slices through the full tomogram) or minislabs (projections of per-particle subvolumes).

Warp

a set of tools for cryo-EM and cryo-ET data processing including, among other tools: Warp, M, WarpTools, MTools, MCore, and Noise2Map.

OpenFold3

is a biomolecular structure prediction model aiming to be a bitwise reproduction of DeepMind's AlphaFold3, developed by the AlQuraishi Lab at Columbia University and the OpenFold consortium. It supports structure prediction of standard and non-canonical protein, RNA, and DNA chains, and small molecules, with pipelines for generating MSAs using ColabFold server or JackHMMER/hhblits following the AlphaFold3 protocol. The tool includes kernel acceleration through cuEquivariance and DeepSpeed4Science kernels, multi-query job support with distributed predictions across multiple GPUs, and performs competitively with state-of-the-art open source biomolecular structure prediction models.

CryoBoltz

is a method for fitting atomic structures into cryo-EM density maps of dynamic proteins. It is built on top of Boltz-1, a state-of-the-art structure prediction model for biomolecular complexes. Through a multi-stage guidance mechanism that modifies the Boltz diffusion trajectory at inference time, CryoBoltz recovers diverse conformations from input cryo-EM data.

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.

ColabFold

an easy-to-use Notebook based environment for fast and convenient protein structure predictions.

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.

CryoAtom

is a software that automatically constructs full-atom 3D structural models of proteins based on cryo-EM density maps and sequence information.

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.

BioEmu

is a model that samples from the approximated equilibrium distribution of structures for a protein monomer, given its amino acid sequence.