SBGrid Consortium homepage

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

a sequence assignment validation tool for in cryo-EM models

REliable PIcking by Consensus (REPIC) is a consensus methodology for harnessing multiple cryogenic-electron microscopy (cryo-EM) particle picking algorithms. It identifies particles common to multiple picked particle sets (i.e., consensus particles) using graph theory and integer linear programming (ILP). Picked particle sets may be found by a human specialist (manual), template matching, mathematical function (e.g., RELION's Laplacian-of-Gaussian auto-picking), or machine-learning method.

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.

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.

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

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.

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.

a sequence assignment validation tool for in cryo-EM models

a software for template matching on tomographic electron microscopy data.