Software Updates

IsoNet2

IsoNet2 is a deep-learning software package for simultaneous missing wedge correction, denoising, and CTF correction in cryo-electron tomography reconstructions using a deep neural network trained on information from the original tomogram(s). Compared to IsoNet1, IsoNet2 produces tomograms with higher resolution and less noise in roughly a tenth of the time. The software requires full tomograms or even/odd paired tomograms as input. Paired tomograms for Noise2Noise training can be split by either frame or tilt.

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.

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.

XDS

(X-ray Detector Software) a software tool for processing single-crystal monochromatic diffraction data recorded by the rotation method.

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.

cryomaskr

is a desktop application that provides WYSIWYG mask generation for cryo-electron microscopy data analysis. It offers an intuitive graphical interface with real-time visual feedback, eliminating the need for complex command-line operations and iterative scripting cycles. The tool integrates with standard cryoEM file formats, and includes advanced masking capabilities for complex structures and membrane proteins.

TomoTwin-cryoet

a deep metric learning based particle picking procedure for cryo-ET

OpenEye Academic Package

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

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.

HADDOCK3

a new open source and modular version of HADDOCK

pytom-match-pick

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

Topaz

a pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz includes methods for micrograph denoising using deep denoising models.

BoltzGen

is a deep learning-based tool for designing protein and peptide binders against target proteins or small molecules.

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.

Ais

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

CUDA

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

Schrodinger

a suite of tools for drug discovery.

CryoAtom

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

ORCA

an electronic structure program package that is a flexible, efficient, and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules.

ResMap

(Resolution Map) a Python (NumPy/SciPy) application with a Tkinter GUI. It is an easy to use software package for computing the local resolution of 3D density maps studied in structural biology, primarily electron cryo-microscopy (cryo-EM). ResMap has a both a GUI (window) and a command line interface.

BindCraft

a user friendly and accurate binder design pipeline.

Google Cloud SDK

a set of tools and libraries for interacting with Google Cloud products and services.

checkMySequence

a sequence assignment validation tool for in cryo-EM models

Google Cloud SDK

a set of tools and libraries for interacting with Google Cloud products and services.

checkMySequence

a sequence assignment validation tool for in cryo-EM models

RDKit

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

checkMySequence

a sequence assignment validation tool for in cryo-EM models

REPIC

REliable PIcking by Consensus (REPIC) is a consensus methodology for harnessing multiple cryogenic-electron microscopy (cryo-EM) particle picking algorithms.