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is a software that automatically constructs full-atom 3D structural models of proteins based on cryo-EM density maps and sequence information. It uses a two-stage approach: first predicting C-alpha atom coordinates from the density map, then building the full-atom model by combining sequence and density information. The tool can work with or without sequence input and includes capabilities for protein refinement, sequence identification from databases, and handling of masked density maps.

a widely used molecular visualization package developed by Warren DeLano, now maintained by Schödinger, LLC. This installation includes official incentive builds of PyMOL.

a tool for exploiting structure hallucination within diffusion for protein design. A fast, fine-tuning-free framework for de novo protein design.

(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.

a self-supervised deep learning framework that works on dense and subtomogram levels. The dense part of the framework is additionally trained on subtasks for tomogram denoising, semantic segmentation (particle identification) and instance segmentation. The subtomogram level part of the method offers embedding representation of the detected particles in the tomogram/s.

an open source, GPL-3.0+ licensed library providing contextual analysis tools for cryo electron tomography and subtomogram averaging.

a pipeline of tools to generate robust open mesh surfaces from voxel segmentations of biological membranes using the Screened Poisson algorithm and calculate morphological features including curvature and membrane-membrane distance using pycurv's vector voting framework with tools to convert these morphological quantities into morphometric insights.

a new web-based user interface for CCP-EM and RELION software.

a supervised machine learning method to directly reconstruct the tomogram from aligned cryo-ET tilt series. The methods is trained on real measurements using FBP+cryo-CARE+IsoNet reconstructions as the reference.

an integrated suite of software tools for processing single particle cryoEM data, from preprocessing raw image data through building and fitting atomic models.