Systematic and Comparative Evaluation of Software Programs for Template-Based Modeling of Protein Structures.

Biotechnology Journal
Woo Dae JangSang Yup Lee

Abstract

Modeling protein structures is critical for understanding protein functions in various biological and biotechnological studies. Among representative protein structure modeling approaches, template-based modeling (TBM) is by far the most reliable and most widely used approach to model protein structures. However, it still remains as a challenge to select appropriate software programs for pairwise alignments and model building, two major steps of the TBM. In this paper, pairwise alignment methods for TBM are first compared with respect to the quality of structure models built using these methods. This comparative study is conducted using comprehensive datasets, which cover 6185 domain sequences from Structural Classification of Proteins extended for soluble proteins, and 259 Protein Data Bank entries (whole protein sequences) from Orientations of Proteins in Membranes database for membrane proteins. Overall, a profile-based method, especially PSI-BLAST, consistently shows high performance across the datasets and model evaluation metrics used. Next, use of two model building programs, MODELLER and SWISS-MODEL, does not seem to significantly affect the quality of protein structure models built except for the Hard group (a group of ...Continue Reading

References

Mar 1, 1970·Journal of Molecular Biology·S B Needleman, C D Wunsch
Mar 25, 1981·Journal of Molecular Biology·T F Smith, M S Waterman
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Feb 9, 2002·Proteins·Arne Elofsson
Apr 21, 2005·Protein Science : a Publication of the Protein Society·Björn Wallner, Arne Elofsson
Jun 9, 2005·Current Opinion in Structural Biology·John Moult
Jan 7, 2006·Bioinformatics·Mikhail A LomizeHenry I Mosberg
Nov 1, 2006·Protein Science : a Publication of the Protein Society·Min-Yi Shen, Andrej Sali
May 19, 2007·Bioinformatics·James A R Dalton, Richard M Jackson
Apr 26, 2008·Current Opinion in Structural Biology·Yang Zhang
Sep 6, 2011·Nucleic Acids Research·Mikhail A LomizeAndrei L Lomize
Jul 21, 2012·Nature Protocols·Morten KällbergJinbo Xu
Mar 8, 2013·PloS One·Marcus StammLucy R Forrest
Jun 12, 2013·Current Protocols in Bioinformatics·William R Pearson
Apr 23, 2014·Nucleic Acids Research·Marcus StammLucy R Forrest
Nov 18, 2014·Nature Methods·Benjamin BuchfinkDaniel H Huson
Jun 21, 2016·Current Protocols in Bioinformatics·Benjamin Webb, Andrej Sali
Dec 3, 2016·Nucleic Acids Research·Milot MirditaMartin Steinegger
May 23, 2018·Nucleic Acids Research·Andrew WaterhouseTorsten Schwede
Aug 9, 2018·ACS Omega·Dmitrii M NikolaevMikhail N Ryazantsev
Sep 7, 2018·Chemical Biology & Drug Design·Muhammed Tilahun Muhammed, Esin Aki-Yalcin
Apr 22, 2019·Cell Systems·Mohammed AlQuraishi
May 12, 2019·International Journal of Molecular Sciences·Recep Adiyaman, Liam James McGuffin
Sep 16, 2019·BMC Bioinformatics·Martin SteineggerJohannes Söding

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Jun 10, 2020·Biotechnology Journal·Min-Kyu OhYu-Chen Hu

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