TCB Publications - Abstract

Ryan McGreevy, Ivan Teo, Abhishek Singharoy, and Klaus Schulten. Advances in the molecular dynamics flexible fitting method for cryo-EM modeling. Methods, 100:50-60, 2016. (PMC: PMC4848153)

MCGR2015 Molecular Dynamics Flexible Fitting (MDFF) is an established technique for fitting all-atom structures of molecules into corresponding cryo-electron microscopy (cryo-EM) densities. The practical application of MDFF is simple but requires the user to be aware of and take measures against a variety of possible challenges presented by each individual case. Some of these challenges arise from the complexity of the molecular structure and the quality of the available structural models used for matching and densities to be interpreted, while others stem from the intricacies of MDFF itself. The current article serves as a guide to navigate through common challenges using strategies that have been developed since MDFF’s inception and to successfully perform MDFF simulations.

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