Software Updates

DOCK

a molecular docking application used to a) predict binding modes of small molecule-protein complexes; b) search databases of ligands for compounds that inhibit enzyme activity, bind a particular protein, bind nucleic acid targets; c) examine possible binding orientations of protein-protein and protein-DNA complexes; d) help guide synthetic efforts by examining small molecules that are computationally derivatized. Dock is offered in the SBGrid collection in two iterations, Dock 3 and Dock 6.

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.

NAMD

a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

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.

Meteor

is a tool for computing crystallographic difference maps that specializes in robust identification of weak signals from minor populations such as bound ligands or time-resolved experimental changes. It maximizes signal-to-noise ratio through structure factor amplitude weighting and TV denoising, while automatically setting parameters using negentropy maximization to minimize user bias. The package provides two command-line scripts for different approaches: meteor.diffmap for fast k-weighted TV-denoised maps and meteor.phaseboost for iterative phase retrieval with potentially better results.

checkMySequence

a sequence assignment validation tool for in cryo-EM models

PyTME

a software for template matching on tomographic electron microscopy data.

BioEmu

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

OpenFold

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

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.

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.

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.

ShapeMapper2

a completely rewritten version of our ShapeMapper for reading out the results of an RNA chemical probing experiment by massively parallel sequencing that integrates careful handling of all classes of adduct-induced sequence changes, sequence variant correction, basecall quality filters, and quality-control warnings to identify RNA adduct sites.

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.

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.

CNIO RELION Tools

a collection of scripts for cryoEM data collection and analysis

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.

Ringer

a program to detect molecular motions by automatic electron density sampling.

OpenEye Academic Package

a package of tools to help design potent and selective bioactive molecules.

CryoAtom

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

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.

PyMOL

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

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.

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.

Protein-Hunter

a tool for exploiting structure hallucination within diffusion for protein design. A fast, fine-tuning-free framework for de novo protein design.

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.

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.

CryoSiam

a self-supervised deep learning framework that works on dense and subtomogram levels. The dense part of the framework is additionally trained on subtasks for tomogram denoising, semantic segmentation (particle identification) and instance segmentation. The subtomogram level part of the method offers embedding representation of the detected particles in the tomogram/s.

cryoCAT

an open source, GPL-3.0+ licensed library providing contextual analysis tools for cryo electron tomography and subtomogram averaging.

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.

Doppio

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

CryoLithe

a supervised machine learning method to directly reconstruct the tomogram from aligned cryo-ET tilt series. The methods is trained on real measurements using FBP+cryo-CARE+IsoNet reconstructions as the reference.

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.

RDKit

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

CNIO RELION Tools

a collection of scripts for cryoEM data collection and analysis