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MAINchain Model trAcing using Spanning Tree from a EM map
MAINMAST directly traces main-chain connections and C-alpha positions by using Tree-Graph models on the EM map.

Reference:
Terashi, G., & Kihara, D. (2018). De novo main-chain modeling for EM maps using MAINMAST. Nature communications, 9(1), 1618.

What is the MAINMAST?

MAINMAST is a de novo modeling protocol to build an entire protein 3D model directly from near-atomic resolution EM map.

MAINMAST is a filly automated protocol and can generate reliable initial C-alpha models which can be used to construct full atomic models. This new de novo modeling method has several advantages; (1) It does not require reference structures; (2) It does not requre manual interventions; (3) a pool of candidate models are generated.

MAINMAST protocol

MAINMAST protocol consists of mainly four steps:

(1) Identify local dense points (LDPs) by Mean Shifting Algorithm;

(2) Connect all LDPs by Minimum Spanning Tree;

(3) Refine Tree structure by Tabu Search algorithm;

(4) Thread sequence on the longest path.

Questions?