Software Updates

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.

RFdiffusion2

is an atom-level enzyme active site scaffolding tool that generates protein backbones conditioned on atomic motifs and small molecules. The software supports enzyme design from atomic motifs with unknown sequence positions, small-molecule binder design with RASA conditioning, and includes integration with LigandMPNN for sequence fitting and Chai1 for structure validation. It provides both indexed backbone and unindexed atomized region outputs with optional idealization steps for enhanced structural quality.

BoltzGen

is a deep learning-based tool for designing protein and peptide binders against target proteins or small molecules. The software uses diffusion models to generate diverse binder candidates, followed by inverse folding, structure prediction with Boltz-2, and comprehensive filtering to select high-quality designs. It supports multiple protocols including protein-anything, peptide-anything, nanobody-anything, and protein-small_molecule design, with automated pipelines that can generate thousands of candidates and rank them based on binding affinity and structural quality metrics.

BoltzDesign

is a molecular design tool powered by the Boltz model for designing protein-protein interactions and biomolecular complexes. It features an end-to-end pipeline that includes sequence optimization using ProteinMPNN/LigandMPNN, structure validation with AlphaFold3, and support for small molecules, DNA, and RNA targets. The tool provides trajectory visualization capabilities and automated setup for complete molecular design workflows.

Rosetta

a software suite for modeling macromolecular structures and for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions.

OpenEye Academic Package

tools to help design potent and selective bioactive molecules.

ANARCI

Antibody Numbering and Antigen Receptor ClassIfication

Icecream

a self-supervised framework for cryo-ET reconstruction that integrates equivariance principles from modern imaging theory into a deep-learning architecture.

OpenFreeEnergy

is a Python package for executing alchemical free energy calculations.

NMRPipe

a set of comprehensive facilities for Fourier processing of spectra in one to four dimensions, as well as a variety of facilities for spectral display and analysis. This is the official NMRScience version of NMRPipe.

MDAnalysis

an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools.

Rosetta

a software suite for modeling macromolecular structures and for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions.

RosEM

a tool that provides easy access to the rosetta cryoem refinement protocol. The pipeline automates testing of different density weights, use of reference/starting model restraints and selections.

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.

PyMOL

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

Warp

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

CTFMeasure

CTFMeasure is a software for estimating CTF parameters of cryo-ET tilt series. It features tilt-series-based joint estimation and Thon ring rescaling technique to retrieve power spectrums with higher SNR and more clear Thon rings, leading to higher estimation accuracy.

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.

SBGrid Installer

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.

nvMolKit

is a CUDA-backed Python library for accelerating common RDKit molecular operations through batch-oriented GPU processing.

pytom-match-pick

a GPU accelerated python module to significantly improve the speed and sensitivity using template matching to detect macromolecules from tomograms.

NGLView

a Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.

RStudio

an integrated development environment (IDE) for R that includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

Napari

a Python library for n-dimensional image visualization, annotation, and analysis.

R

a free software environment for statistical computing and graphics.

PowerFit

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

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.

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.

OpenFreeEnergy

is a Python package for executing alchemical free energy calculations.

Spring

(Single Particle Reconstruction from Images of kNown Geometry) a single-particle based helical reconstruction package for electron cryo-micrographs used to determine 3D structures of either highly ordered or less ordered specimens.

RoseTTAFold2

a tool that extends the original three-track architecture of RoseTTAFold over the full network, incorporating the concepts of Frame-aligned point error, recycling during training, and the use of a distillation set from AlphaFold2.

RDKit

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

SimpleFold

is the first flow-matching based protein folding model that uses only general purpose transformer layers, without relying on expensive modules like triangle attention or pair representation biases.

IsoNet

(ISOtropic reconstructioN of Electron Tomography) a tool that trains deep convolutional neural networks to reconstruct meaningful contents in the missing wedge for electron tomography, and to increase signal-to-noise ratio, using the information learned from the original tomogram.

Boltz-1

an open-source model which predicts the 3D structure of proteins, rna, dna and small molecules; it handles modified residues, covalent ligands and glycans, as well as condition the generation on pocket residues.