Software Updates

AF3Complex

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.

AlphaPulldown

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

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.

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.

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

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.

ColabFold

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

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.

PyMOL

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