Abstract
Segment assembly, structure alignment and iterative simulation in protein structure prediction
Highlights
It has been 50 years since Anfinsen first showed that the native structure of protein molecules is determined solely by their amino acid sequence, with the folded state representing a unique and kinetically accessible mini mum of the free energy [1]
More pronounced topology-level improvements were achieved when new structural templates identified from the Protein Data Bank (PDB) were incorporated into the folding iterations; these templates were detected by the structure alignment program TMalign [6], which matches the TASSER models with each of the known proteins in the PDB to identify the templates that are structurally closest to the TASSER models
In the development of FG-MD (Fragment Guided-Molecular Dynamics simulation) [7], a method for atomic-level structural refinements, the initial models to be refined are split into segments spanning two to four secondary structure elements; template segment structures similar to that split from the initial models are identified from the PDB library by TM-align
Summary
It has been 50 years since Anfinsen first showed that the native structure of protein molecules is determined solely by their amino acid sequence, with the folded state representing a unique and kinetically accessible mini mum of the free energy [1]. *Correspondence: zhng@umich.edu 1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA Full list of author information is available at the end of the article structure assembly and refinement of protein molecules [5].
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