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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.

is a model that samples from the approximated equilibrium distribution of structures for a protein monomer, given its amino acid sequence.

a trainable, memory-efficient, and GPU-friendly PyTorch reproduction of DeepMind's AlphaFold 2.

(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.

is a deep learning-based tool for designing protein and peptide binders against target proteins or small molecules. The software uses diffusion models to generate diverse binder candidates, followed by inverse folding, structure prediction with Boltz-2, and comprehensive filtering to select high-quality designs. It supports multiple protocols including protein-anything, peptide-anything, nanobody-anything, and protein-small_molecule design, with automated pipelines that can generate thousands of candidates and rank them based on binding affinity and structural quality metrics.