TMDIM: an improved algorithm for the structure prediction of
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TMDIM: an improved algorithm for the structure prediction of
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J Comput Aided Mol Des DOI 10.1007/s10822-017-0047-0
TMDIM: an improved algorithm for the structure prediction of transmembrane domains of bitopic dimers Han Cao1 · Marcus C. K. Ng1 · Siti Azma Jusoh2 · Hio Kuan Tai1 · Shirley W. I. Siu1
Abstract 𝛼 -Helical transmembrane proteins are the most important drug targets in rational drug development. However, solving the experimental structures of these proteins remains difficult, therefore computational methods to accurately and efficiently predict the structures are in great demand. We present an improved structure prediction method TMDIM based on Park et al. (Proteins 57:577–585, 2004) for predicting bitopic transmembrane protein dimers. Three major algorithmic improvements are introduction of the packing type classification, the multiple-condition decoy filtering, and the cluster-based candidate selection. In a test of predicting nine known bitopic dimers, approximately 78% of our predictions achieved a successful fit (RMSD
