SBGridTV
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.
a series of software tools for docking flexible ligands into receptors with selective flexibility, comprising: 1) AutoDockFR: a docking engine using the AutoDock4 forcefield; 2) AutoGridFR: a graphical user interface for setting up docking boxes; 3) AutoSite: a ligand binding site detection and characterization program.
(Crystallographic Object-Oriented Toolkit) 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.
a suite of programs that allows users to carry out molecular dynamics simulations, particularly on biomolecules. The suite can be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB) with either explicit water or generalized Born solvent models. The independently developed packages work well by themselves, and with Amber itself.
(Hypergeometric Optimization of Motif EnRichment) a suite of sequencing analysis and sequence motif discovery tools.
a program for analysis of SAXS data that enables creation of 1D scattering profiles from 2D detector images, standard data operations such as averaging and subtraction, analysis of radius of gyration (Rg) and molecular weight, and advanced processing using GNOM, DAMMIF, and AMBIMETER. It also allows easy processing of inline SEC-SAXS data.
ligand binding site prediction from protein sequence and structure.
a GUI (graphical user interface) for XDS designed to help both novice and experienced users; it enables XDS data processing without the command line and supplies additional graphical information in a simple, user-modifiable and user-extensible way. It graphically displays the ASCII and cbf files that XDS writes and can run useful shell commands with a simple mouse click.
a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
a tool to predict protein structure, function, and mutations using evolutionary sequence covariation.
a neural network for the automatic identification of oligonucleotides and protein secondary structure in cryo‐EM maps.
is a new version of Sparky renamed because NMRFAM, through the generous allowance of Tom Ferrin and Tom Goddard of UCSF, has taken over the original Sparky for continuous development to support advances in the biomolecular NMR field.
(Diffraction Integration for Advanced Light Sources) a software project for the analysis of crystallographic diffraction images for many new methods from shutterless, fine-sliced rotation scans to randomly-oriented snapshots of serial crystallography. It uses multiple CPU and GPU machines to increase speed and accuracy based on a comprehensive physical model.
