SBGridTV
(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 suite of tools for drug discovery. The Schrodinger suite runs on Linux and Mac workstations, but due to its size, it is not included in our default installation.
an image processing framework to obtain 3D models of macromolecular complexes using 3D EM that allows you to execute workflows combining different software tools, while taking care of formats and conversions.
(Particle Estimation for Electron Tomography) a package for aligning and averaging particles in 3-D subvolumes extracted from tomograms. If PEET and IMOD are both installed, most PEET operations are available from the eTomo graphical user interface in IMOD. PEET is written in Matlab and a compiled version is distributed along with the Matlab runtime environment needed to run it.
Doppio is a new web-based user interface for CCP-EM and RELION software.
a deep learning based protein sequence design method.
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.
pdb-images is a command-line tool from PDBe EMBL-EBI for generating images of macromolecular structures from mmCIF or binary CIF structure files based on Mol*.
GTalign is a novel high-performance protein structure alignment, superposition and search method with flexible structure clustering ability.
an open-source model which predicts the 3D structure of proteins, rna, dna and small molecules; it handles modified residues, covalent ligands and glycans, as well as condition the generation on pocket residues.
OpenNucleome is an open-source software designed for conducting molecular dynamics (MD) simulations of the human nucleus. This software streamlines the process of setting up whole nucleus simulations through just a few lines of Python scripting.
a widely used molecular visualization package developed by Warren DeLano, now maintained by Schödinger, LLC. This installation includes official incentive builds of PyMOL.
