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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.

Terashi, Genki, and Daisuke Kihara. "De novo main-chain modeling for EM maps using MAINMAST." Nature communications 9.1 (2018): 1618.
Terashi, Genki, and Daisuke Kihara. "De novo main-chain modeling with MAINMAST in 2015/2016 EM Model Challenge." Journal of structural biology 204.2 (2018): 351-359.


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.