Protein Structural Modeling for Electron Microscopy Maps Using VESPER and MAINMAST

An increasing number of protein structures are determined by cryo‐electron microscopy (cryo‐EM) and stored in the Electron Microscopy Data Bank (EMDB). To interpret determined cryo‐EM maps, several methods have been developed that model the tertiary structure of biomolecules, particularly proteins. Here we show how to use two such methods, VESPER and MAINMAST, which were developed in our group. VESPER is a method mainly for two purposes: fitting protein structure models into an EM map and aligning two EM maps locally or globally to capture their similarity. VESPER represents each EM map as a set of vectors pointing toward denser points. By considering matching the directions of vectors, in general, VESPER aligns maps better than conventional methods that only consider local densities of maps. MAINMAST is a de novo protein modeling tool designed for EM maps with resolution of 3–5 Å or better. MAINMAST builds a protein main chain directly from a density map by tracing dense points in an EM map and connecting them using a tree‐graph structure. This article describes how to use these two tools using three illustrative modeling examples. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Protein structure model fitting using VESPER Alternate Protocol: Atomic model fitting using VESPER web server Basic Protocol 2: Protein de novo modeling using MAINMAST