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.
a program suite (hbplus, access and clean) to compute hydrogen positions, hydrogen bonds, and neighboring interactions. The application was developed at University College London.
a set of tools and libraries for interacting with Google Cloud products and services.
an assembly line of macromolecular assemblies, Assembline is a multi-step protocol for integrative structural modeling of macromolecular complexes based on electron microscopy, cross-linking mass spectrometry and other data.
Scipion is an open-source cryo-EM workflow platform that supports complete SPA and Tomography pipelines, from raw movies or tilt-series movies to final post-processed maps. It combines Xmipp algorithms with leading cryo-EM software. It can complement or provide an alternative to full-pipeline packages such as RELION and cryoSPARC, while taking care of formats and conversions in a completely transparent way for the user.
an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.
(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.
(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.
(Alignment and Reconstruction for Electron Tomography) is a GPU-accelerated software package that provides an integrated solution to both fiducial-free alignment and reconstruction for cryoEM tomography.
(Intrinsically Disordered Proteins Conformer Generator) a flexible, modular platform for generating ensembles of disordered protein states that builds conformers by sampling backbone torsion angles of relevant sequence fragments extracted from protein structures in the RCSB Protein Data Bank.
a python module for calculating paramagnetic effects in NMR spectra of proteins. This currently includes fitting of paramagnetic susceptibility tensors to experimental data associated with pseudocontact shifts (PCS) residual dipolar couplings (RDC), paramagnetic relaxation enhancements (PRE) and cross-correlated relaxation (CCR). A GUI allows easy viewing of data and seamless transition between PCS/RDC/PRE/CCR calculations.
