SBGridTV
(REgularised LIkelihood OptimisatioN) a stand-alone computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.
a Python implementation of the STAR file format designed principally for compatibility with RELION format STAR files. It allows STAR files to be created and opened easily using a very simple API, exposing data blocks as pandas DataFrame objects.
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 high quality visualizer and annotator for three dimensional molecular structures, sequences, alignments, chemical spreadsheets and biological data.
(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.
a software system containing crystallographic structure refinement using Bayesian statistical methods (BUSTER), ligand fitting (rhofit) and a fully automated pipeline (Pipedream) to drive a structure based fragment/ligand screening pathway.
an interface for cryo-transmission electron microscopy (cryo-EM) data collection with computer image processing. Focus creates a user-friendly environment to import and manage data recorded by direct electron detectors and perform elemental image processing tasks in a high-throughput manner, while new data is being acquired at the microscope.
(Collaborative Computational Project for Electron cryo-Microscopy) a software framework and resulting software suite that includes tools for project and data management along with a focus on building and refinement of atomic models into cryo-EM reconstructions. The framework allows easy access to various programs and utilities from collaborators via Python task wrappers and a user-friendly graphical user interface or a command-line interface suitable for scripting.
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.
