Software Updates

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.

TranSPHIRE

a software package for fully automated processing of cryo-EM data sets during data acquisition. TranSPHIRE transfers data from the microscope, automatically applies the common pre-processing steps, picks particles, performs 2D clustering and 3D refinement parallel to image recording. Importantly, TranSPHIRE introduces a machine learning-based feedback loop to re-train its internally used picking model to adapt to any given data set live during processing. This elegant approach enables TranSPHIRE to process data more effectively, producing high-quality particle stacks. TranSPHIRE collects and displays all microscope settings and metrics generated by its individual tools in order to allow users to quickly evaluate data during acquisition. TranSPHIRE can run on a single work station and also includes the automated processing of filaments.

jq

a lightweight and flexible command-line JSON processor.

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.

CcpNmr Analysis

a series of programs for macromolecular NMR including AnalysisAssign, AnalysisScreen, AnalysisMetabolomics and AnalysisStructure, and with version 3, the addition CcpNmr ChemBuild.

KLT picker

(Karhunen Loeve Transform picker) a fully automatic EM particle picker and requires only the approximated particle size as an input . It is especially designed to handle low SNR micrographs. It is based on learning a set of optimal templates through the use of multi-variate statistical analysis via the Karhunen Loeve Transform.

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.

Illustrate

a small Fortran program for creating non-photorealistic illustrations of molecules, with cartoony colors and outlines, and soft ambient shadows. I originally developed it during postdoctoral training in the laboratory of Arthur J. Olson at the Scripps Research Institute, and have tinkered with it ever since. I have used it to create materials for my books and for PDB-101, the outreach portal of the RCSB Protein Data Bank, most notably, for the “Molecule of the Month.”

Xplor-NIH

a package for biomolecular structure determination from experimental NMR data combined with known geometric data. Xplor–NIH was derived from XPLOR version 3.851 and contains all of the functionality therein in addition to numerous new features designed to render a highly flexible architecture and foster the rapid and easy development of new functionality.