Software Updates

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.

SAMtools

(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.

TomoDRGN

a tool that extends the cryoDRGN framework to cryo-ET by learning heterogeneity from datasets in which each particle is sampled by multiple projection images at different stage tilt angles.

tomoCPT

is a deep learning based program for enabling centroid prediction of objects in 3D cryo-tomograms.

CryoAtom

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

PyMOL

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

MassiveFold

a tool designed to expand structure prediction sampling by optimizing the parallelization of AlphaFold-based predictions across GPU clusters.

AlphaPulldown

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

PEET

(Particle Estimation for Electron Tomography) a package for aligning and averaging particles in 3-D subvolumes extracted from tomograms. If PEET and IMOD are both installed, most PEET operations are available from the eTomo graphical user interface in IMOD. PEET is written in Matlab and a compiled version is distributed along with the Matlab runtime environment needed to run it.

AreTomo3

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

Global Phasing Suite

a program that combines installation of autoPROC, BUSTER, and SHARP available to Global Phasing consortium members.

BUSTER

a software system containing crystallographic structure refinement using Bayesian statistical methods (BUSTER), ligand fitting (rhofit) and a fully automated pipeline (Pipedream) to drive a structure based fragment/ligand screening pathway.

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.

IMOD

a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections.

ESM

is a protein modelling package providing ESMC, a protein language model trained on billions of sequences, and ESMFold2, which predicts all-atom protein structures from amino acid sequences with optional multiple sequence alignments. The models support protein sequence analysis, structure prediction, protein-complex modelling, and protein binder design, with pretrained weights available for local use.

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.

CryoAtom

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

CUDA

a tool that helps redistributable software libraries to support CUDA applications for Linux.

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.

PEET

(Particle Estimation for Electron Tomography) a package for aligning and averaging particles in 3-D subvolumes extracted from tomograms. If PEET and IMOD are both installed, most PEET operations are available from the eTomo graphical user interface in IMOD. PEET is written in Matlab and a compiled version is distributed along with the Matlab runtime environment needed to run it.

CryoCodex

is a tool for cryo-EM density maps, estimating local map quality, and predicting molecular masks. It produces an enhanced map, local quality scores for both the original and enhanced maps, and a molecular mask to support map interpretation and structural analysis. It offers a faster cropped-map processing mode and full-map processing.

Careless

a tool that merges crystallography data without much physics. It performs scaling, merging, and French-Wilson corrections in a single step by directly inferring structure factor amplitudes from unscaled, unmerged intensities.

BioXTAS RAW

a program for analysis of SAXS data that enables creation of 1D scattering profiles from 2D detector images, standard data operations such as averaging and subtraction, analysis of radius of gyration (Rg) and molecular weight, and advanced processing using GNOM, DAMMIF, and AMBIMETER. It also allows easy processing of inline SEC-SAXS data.

OpenFreeEnergy

is a Python package for executing alchemical free energy calculations.

cs2star

a simple utility that wraps around csparc2star.py to convert particle positions from Cryosparc JOB directories into a RELION-ready directory.

AlphaPulldown

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

cs2star

a simple utility that wraps around csparc2star.py to convert particle positions from Cryosparc JOB directories into a RELION-ready directory.

EPU_group_AFIS (Ratolon's Fork)

a tool that takes the XML metadata from an EPU session that used AFIS (Aberration Free Image Shift) for faster acquisition and organizes the collected micrograph movies into RELION Optics Groups. In RELION version 3.1 where these groups were introduced they can be used to further reduce the effects of high-order aberrations on the data induced by using large amounts of beam-image shift.

NMRFx Analyst

a tool for NMR processing, visualization and analysis that integrates code of NMRFx Processor, Structure and additional tools.

Ais

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

DSSP

a program that standardizes secondary structure assignment calculated from a coordinate file. Secondary structure prediction is not supported. Designed by Wolfgang Kabsch and Chris Sander

cryoFILTER

is a cryo-EM contamination detection and particle-filtering tool that identifies contaminated regions in micrographs without discarding entire images. It can classify contamination such as carbon, crystalline ice, aggregates, and ethane, and filter affected particle picks through integration with CryoSPARC and RELION. It also provides a browser-based interface for annotation and fine-tuning models on individual datasets.

autoPROC

a tool that combines third-party processing programs with new tools for automated data processing of single-sweep, multi-sweep and multi-crystal X-ray diffraction data.

BindCraft2

brings de novo miniproteins, scaffolded binders, cyclic peptides and multistate design into one workflow. Describe your target, choose the kind of binder you want, and add properties that matter for your experiment. Named presets supply the design settings and acceptance filters; you can adjust individual settings when needed.

autoPROC

a tool that combines third-party processing programs with new tools for automated data processing of single-sweep, multi-sweep and multi-crystal X-ray diffraction data.

BindCraft2

brings de novo miniproteins, scaffolded binders, cyclic peptides and multistate design into one workflow. Describe your target, choose the kind of binder you want, and add properties that matter for your experiment. Named presets supply the design settings and acceptance filters; you can adjust individual settings when needed.

AlphaPulldown

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

Volume_Seg_Tool

a tool that utilizes deep learning to perform volumetric electron microscopy image segmentations, both semantic and instance segmentation.