A supersecondary structure library and search algorithm for modeling loops in protein structures.

Nucleic Acids Research
Narcis Fernandez-FuentesAndrás Fiser

Abstract

We present a fragment-search based method for predicting loop conformations in protein models. A hierarchical and multidimensional database has been set up that currently classifies 105,950 loop fragments and loop flanking secondary structures. Besides the length of the loops and types of bracing secondary structures the database is organized along four internal coordinates, a distance and three types of angles characterizing the geometry of stem regions. Candidate fragments are selected from this library by matching the length, the types of bracing secondary structures of the query and satisfying the geometrical restraints of the stems and subsequently inserted in the query protein framework where their fit is assessed by the root mean square deviation (r.m.s.d.) of stem regions and by the number of rigid body clashes with the environment. In the final step remaining candidate loops are ranked by a Z-score that combines information on sequence similarity and fit of predicted and observed phi/psi main chain dihedral angle propensities. Confidence Z-score cut-offs were determined for each loop length that identify those predicted fragments that outperform a competitive ab initio method. A web server implements the method, regula...Continue Reading

References

Nov 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·S Henikoff, J G Henikoff
Feb 20, 1992·Journal of Molecular Biology·A S Kolaskar, U Kulkarni-Kale
Nov 1, 1990·Trends in Biochemical Sciences·M SarasteA Wittinghofer
Dec 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·A C MartinA R Rees
Aug 20, 1987·Journal of Molecular Biology·C Chothia, A M Lesk
Dec 25, 1981·Journal of Molecular Biology·J Greer
Feb 1, 1995·Current Opinion in Structural Biology·J A TainerR P Cunningham
Dec 5, 1993·Journal of Molecular Biology·A Sali, T L Blundell
Sep 5, 1993·Journal of Molecular Biology·L Holm, C Sander
Jan 12, 1996·Journal of Molecular Biology·R T WintjensS J Wodak
Mar 7, 1997·Journal of Molecular Biology·B OlivaM J Sternberg
Jun 1, 1997·Protein Engineering·U Lessel, D Schomburg
Nov 25, 1997·Biophysical Journal·J L Pellequer, S W Chen
Mar 6, 1998·Protein Engineering·E Azarya-SprinzakR Nussinov
Mar 6, 1998·Protein Engineering·K GunasekaranP Balaram
Jul 2, 1999·Journal of Molecular Biology·J TsaiM Gerstein
Aug 19, 1999·Proteins·U Lessel, D Schomburg
Mar 29, 2000·Journal of Molecular Biology·F S DominguesM J Sippl
Oct 25, 2000·Protein Science : a Publication of the Protein Society·A FiserA Sali
Mar 20, 2001·Journal of Molecular Biology·J D Blake, F E Cohen
Apr 5, 2001·Journal of Molecular Biology·A E ToddJ M Thornton
May 10, 2001·Protein Science : a Publication of the Protein Society·C M Deane, T L Blundell
Aug 28, 2001·Protein Engineering·D F Burke, C M Deane
Oct 6, 2001·Science·D Baker, A Sali
Dec 14, 2001·Protein Science : a Publication of the Protein Society·David Shortle
Dec 26, 2001·Nucleic Acids Research·Alex BatemanErik L L Sonnhammer
May 2, 2002·Protein Engineering·Silvio C E TosattoReinhard Männer
May 9, 2002·Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme·Masami Kusunoki
May 29, 2002·Proceedings of the National Academy of Sciences of the United States of America·Zhexin XiangBarry Honig

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Citations

Jun 28, 2011·Journal of Chemical Information and Modeling·Yaohang LiEric Jakobsson
Feb 23, 2012·The Journal of Physical Chemistry. B·A Subramani, C A Floudas
Oct 25, 2011·Nucleic Acids Research·Joan SeguraNarcis Fernandez-Fuentes
Oct 30, 2008·Protein Engineering, Design & Selection : PEDS·Meng CuiRoman Osman
Feb 20, 2009·Journal of Bioinformatics and Computational Biology·Miguel M F Bugalho, Arlindo L Oliveira
Jul 6, 2006·BMC Structural Biology·Narcis Fernandez-Fuentes, András Fiser
Aug 22, 2009·PLoS Computational Biology·Pu LiuDimitris K Agrafiotis
Apr 28, 2010·PLoS Computational Biology·Narcis Fernandez-FuentesAndras Fiser
Oct 23, 2013·PloS One·Ivan Kalev, Michael Habeck
May 3, 2013·PeerJ·Yoonjoo ChoiCharlotte M Deane
Nov 23, 2013·Nucleic Acids Research·Jaume BonetBaldo Oliva
Jun 21, 2011·Current Opinion in Structural Biology·Erik VerschuerenJoost Schymkowitz
Jul 17, 2009·Protein Science : a Publication of the Protein Society·Manoj TyagiAlexandre G de Brevern
Mar 6, 2009·Journal of Computational Chemistry·Dongsheng ZouJingyuan He
Jul 24, 2010·Journal of Computational Chemistry·Dongsheng ZouYuxian Xia
Dec 30, 2014·Bioinformatics·Baldo Oliva, Narcis Fernandez-Fuentes
Apr 16, 2013·Biochimie·Jaroslav KubrychtJiří Hudeček
Aug 8, 2015·PLoS Computational Biology·Brinda VallatAndras Fiser
Aug 29, 2012·Molecular Biology International·Jaroslav KubrychtPavel Souček
Aug 9, 2016·Journal of Molecular Biology·Bhadrachalam ChitturiNick V Grishin
Nov 5, 2016·Proceedings of the National Academy of Sciences of the United States of America·Craig O MackenzieGevorg Grigoryan
Aug 22, 2012·Acta Biochimica Et Biophysica Sinica·Jingli HouJianhua Liu
Apr 23, 2008·Current Protocols in Protein Science·Narayanan EswarAndrej Sali
Apr 23, 2008·Current Protocols in Bioinformatics·Narayanan EswarAndrej Sali
Jan 25, 2019·Biological Chemistry·Kale Kundert, Tanja Kortemme
Feb 20, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Eva MartinsRenata Silva
May 2, 2017·Current Opinion in Structural Biology·Craig O Mackenzie, Gevorg Grigoryan
Mar 1, 2008·Journal of Chemical Theory and Computation·Matthew S Lin, Teresa Head-Gordon

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Methods Mentioned

BETA
X-ray
NMR

Software Mentioned

ArchPRED
ModLoop
CHARMM
CONGEN
FREAD
FUGUE
CODA
DSSP

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