Software Updates

PDB Validation Suite

a set of tools used by the PDB for processing and checking structure data.

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.

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.

Dynamo

a software environment for subtomogram averaging of cryo-EM data.

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.

MoRDa

a pipeline for molecular replacement protein structure solution using X-ray data. The software package includes a database and a set of programs for the structure solution.

PROPKA

a tool that predicts the pKa values of ionizable groups in proteins (version 3.0) and protein-ligand complexes (version 3.1 and later) based on the 3D structure.

PHENIX

(Python-based Hierarchical Environment for INtegrated Xtallography) a software suite for the automated determination of molecular structures using X-ray crystallography and other methods.

PyEM

a set of Python modules and command-line utilities for electron microscopy of biological samples.

ISOLDE

an immersive environment designed to ease the task of building high quality macromolecular models into low to medium resolution experimental maps, where the experimental information alone is insufficient to place individual atoms precisely. ISOLDE is implemented as a plugin to ChimeraX and can be conveniently installed via its built-in Tool Shed.

NMRFx Processor

a software for processing multi-dimensional NMR spectra featuring quality and performance to handle complex data analyses.

IGV

(Integrative Genomics Viewer) a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

NMRFx Processor

a software for processing multi-dimensional NMR spectra featuring quality and performance to handle complex data analyses.