Topology-independent and global protein structure alignment through an FFT-based algorithm

Bioinformatics
Zeyu WenSheng-You Huang

Abstract

Protein structure alignment is one of the fundamental problems in computational structure biology. A variety of algorithms have been developed to address this important issue in the past decade. However, due to their heuristic nature, current structure alignment methods may suffer from suboptimal alignment and/or over-fragmentation and thus lead to a biologically wrong alignment in some cases. To overcome these limitations, we have developed an accurate topology-independent and global structure alignment method through an FFT-based exhaustive search algorithm, which is referred to as FTAlign. Our FTAlign algorithm was extensively tested on six commonly used datasets and compared with seven state-of-the-art structure alignment approaches, TMalign, DeepAlign, Kpax, 3DCOMB, MICAN, SPalignNS and CLICK. It was shown that FTAlign outperformed the other methods in reproducing manually curated alignments and obtained a high success rate of 96.7 and 90.0% on two gold-standard benchmarks, MALIDUP and MALISAM, respectively. Moreover, FTAlign also achieved the overall best performance in terms of biologically meaningful structure overlap (SO) and TMscore on both the sequential alignment test sets including MALIDUP, MALISAM and 64 difficult...Continue Reading

References

Mar 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·E Katchalski-KatzirI A Vakser
Sep 5, 1993·Journal of Molecular Biology·L Holm, C Sander
Jan 1, 1996·Methods in Enzymology·C A Orengo, W R Taylor
Sep 1, 1996·Protein Engineering·N N Alexandrov
Jun 1, 1997·Current Opinion in Structural Biology·Y Lindqvist, G Schneider
Aug 15, 1997·Structure·C A OrengoJ M Thornton
Oct 31, 1998·Protein Engineering·I N Shindyalov, P E Bourne
Aug 24, 1999·Journal of Molecular Biology·T C Wood, W R Pearson
Aug 31, 2000·Protein Engineering·J Jung, B Lee
Feb 13, 2001·Protein Engineering·P LacknerF S Domingues
Jun 19, 2001·Current Opinion in Structural Biology·P Koehl
Feb 13, 2002·Current Opinion in Structural Biology·Olivier Lichtarge, Mathew E Sowa
Oct 17, 2002·Journal of Molecular Biology·Rachel KolodnyMichael Levitt
Nov 5, 2002·Biophysical Journal·Hin Hark GanTamar Schlick
Jun 5, 2003·Proteins·Joël JaninUNKNOWN Critical Assessment of PRedicted Interactions
Jun 26, 2003·Nucleic Acids Research·Adam Zemla
Jul 12, 2003·Bioinformatics·O DrorH Wolfson
Dec 19, 2003·Nucleic Acids Research·Lucy A Stebbings, Kenji Mizuguchi
May 19, 2004·Journal of Molecular Biology·A C CamprouxP Tufféry
Jun 25, 2004·Nucleic Acids Research·Yuzhen Ye, Adam Godzik
Dec 21, 2004·Proteins·Jianhua Zhu, Zhiping Weng
Apr 26, 2005·Nucleic Acids Research·Yang Zhang, Jeffrey Skolnick
Jun 9, 2005·Bioinformatics·Dmitry LupyanAngel R Ortiz
Jun 1, 2006·Proteins·Arun S KonagurthuArthur M Lesk
Nov 23, 2006·BMC Bioinformatics·Bjoern KolbeckErnst-Walter Knapp
Jan 16, 2007·Structure·Matthew Bashton, Cyrus Chothia
Aug 4, 2007·BMC Structural Biology·Gabriele MayrPeter Lackner
Sep 15, 2007·Nucleic Acids Research·Hua ChengNick V Grishin
Nov 16, 2007·Proteins·M TyagiB Offmann
Jan 1, 2008·Proceedings of the National Academy of Sciences of the United States of America·Michal Brylinski, Jeffrey Skolnick
Apr 4, 2008·Proceedings of the National Academy of Sciences of the United States of America·Lei Xie, Philip E Bourne
May 9, 2008·Journal of Bioinformatics and Computational Biology·Sheng Wang, Wei-Mou Zheng
Dec 17, 2008·BMC Bioinformatics·Shashi Bhushan Pandit, Jeffrey Skolnick
Jun 2, 2009·Current Opinion in Structural Biology·Hitomi Hasegawa, Liisa Holm
Jun 10, 2009·Journal of Bioinformatics and Computational Biology·Saeed SalemChristopher Bystroff
Jul 10, 2009·Protein Engineering, Design & Selection : PEDS·M S MadhusudhanAndrej Sali
Jan 1, 2008·Computational Systems Bioinformatics·Saeed Salem, Mohammed J Zaki
Aug 21, 2009·Bioinformatics·Cristian Micheletti, Henri Orland
Jan 6, 2010·Algorithms for Molecular Biology : AMB·Saeed SalemChris Bystroff
Feb 6, 2010·Proceedings of the National Academy of Sciences of the United States of America·Inbal Budowski-TalRachel Kolodny
Feb 19, 2010·Bioinformatics·Jinrui Xu, Yang Zhang
May 21, 2011·Nucleic Acids Research·Minh N Nguyen, M S Madhusudhan

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.