BioShell-Threading: Versatile Monte Carlo Package for Protein 3D Threading

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2014 Jan 22

PMID 24444459

Citations 7

Authors

Pawel Gniewek

Andrzej Kolinski

Andrzej Kloczkowski

Dominik Gront

Affiliations

Soon will be listed here.

Abstract

Background: The comparative modeling approach to protein structure prediction inherently relies on a template structure. Before building a model such a template protein has to be found and aligned with the query sequence. Any error made on this stage may dramatically affects the quality of result. There is a need, therefore, to develop accurate and sensitive alignment protocols.

Results: BioShell threading software is a versatile tool for aligning protein structures, protein sequences or sequence profiles and query sequences to a template structures. The software is also capable of sub-optimal alignment generation. It can be executed as an application from the UNIX command line, or as a set of Java classes called from a script or a Java application. The implemented Monte Carlo search engine greatly facilitates the development and benchmarking of new alignment scoring schemes even when the functions exhibit non-deterministic polynomial-time complexity.

Conclusions: Numerical experiments indicate that the new threading application offers template detection abilities and provides much better alignments than other methods. The package along with documentation and examples is available at: http://bioshell.pl/threading3d.

Citing Articles

Contact-Assisted Threading in Low-Homology Protein Modeling.

Bhattacharya S, Roche R, Shuvo M, Moussad B, Bhattacharya D Methods Mol Biol. 2023; 2627:41-59.

PMID: 36959441 PMC: 10340115. DOI: 10.1007/978-1-0716-2974-1_3.

Recent Advances in Protein Homology Detection Propelled by Inter-Residue Interaction Map Threading.

Bhattacharya S, Roche R, Shuvo M, Bhattacharya D Front Mol Biosci. 2021; 8:643752.

PMID: 34046429 PMC: 8148041. DOI: 10.3389/fmolb.2021.643752.

Prediction of Protein Tertiary Structure via Regularized Template Classification Techniques.

Alvarez-Machancoses O, Fernandez-Martinez J, Kloczkowski A Molecules. 2020; 25(11).

PMID: 32466409 PMC: 7321371. DOI: 10.3390/molecules25112467.

Practical Considerations for Atomistic Structure Modeling with Cryo-EM Maps.

Kim D, Gront D, Sanbonmatsu K J Chem Inf Model. 2020; 60(5):2436-2442.

PMID: 32422044 PMC: 7891309. DOI: 10.1021/acs.jcim.0c00090.

Predicting protein tertiary structure and its uncertainty analysis via particle swarm sampling.

Alvarez O, Fernandez-Martinez J, Corbeanu A, Fernandez-Muniz Z, Kloczkowski A J Mol Model. 2019; 25(3):79.

PMID: 30810816 PMC: 7586042. DOI: 10.1007/s00894-019-3956-0.

References

Henikoff S, Henikoff J . Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A. 1992; 89(22):10915-9. PMC: 50453. DOI: 10.1073/pnas.89.22.10915. View

Cheng H, Kim B, Grishin N . MALIDUP: a database of manually constructed structure alignments for duplicated domain pairs. Proteins. 2007; 70(4):1162-6. DOI: 10.1002/prot.21783. View

Mirny L, Shakhnovich E . Protein structure prediction by threading. Why it works and why it does not. J Mol Biol. 1998; 283(2):507-26. DOI: 10.1006/jmbi.1998.2092. View

Swendsen , Wang . Nonuniversal critical dynamics in Monte Carlo simulations. Phys Rev Lett. 1987; 58(2):86-88. DOI: 10.1103/PhysRevLett.58.86. View

Xu J, Li M, Kim D, Xu Y . RAPTOR: optimal protein threading by linear programming. J Bioinform Comput Biol. 2004; 1(1):95-117. DOI: 10.1142/s0219720003000186. View

Remmert M, Biegert A, Hauser A, Soding J . HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Methods. 2011; 9(2):173-5. DOI: 10.1038/nmeth.1818. View

Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W . Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997; 25(17):3389-402. PMC: 146917. DOI: 10.1093/nar/25.17.3389. View

Farrar M . Striped Smith-Waterman speeds database searches six times over other SIMD implementations. Bioinformatics. 2006; 23(2):156-61. DOI: 10.1093/bioinformatics/btl582. View

Holm L, Sander C . Protein structure comparison by alignment of distance matrices. J Mol Biol. 1993; 233(1):123-38. DOI: 10.1006/jmbi.1993.1489. View

10.

Soding J . Protein homology detection by HMM-HMM comparison. Bioinformatics. 2004; 21(7):951-60. DOI: 10.1093/bioinformatics/bti125. View

11.

Domingues F, Lackner P, Andreeva A, Sippl M . Structure-based evaluation of sequence comparison and fold recognition alignment accuracy. J Mol Biol. 2000; 297(4):1003-13. DOI: 10.1006/jmbi.2000.3615. View

12.

Marti-Renom M, Madhusudhan M, Sali A . Alignment of protein sequences by their profiles. Protein Sci. 2004; 13(4):1071-87. PMC: 2280052. DOI: 10.1110/ps.03379804. View

13.

Mittelman D, Sadreyev R, Grishin N . Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments. Bioinformatics. 2003; 19(12):1531-9. DOI: 10.1093/bioinformatics/btg185. View

14.

Lobley A, Sadowski M, Jones D . pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination. Bioinformatics. 2009; 25(14):1761-7. DOI: 10.1093/bioinformatics/btp302. View

15.

Miyazawa S, Jernigan R . Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol. 1996; 256(3):623-44. DOI: 10.1006/jmbi.1996.0114. View

16.

Gront D, Blaszczyk M, Wojciechowski P, Kolinski A . BioShell Threader: protein homology detection based on sequence profiles and secondary structure profiles. Nucleic Acids Res. 2012; 40(Web Server issue):W257-62. PMC: 3394251. DOI: 10.1093/nar/gks555. View

17.

Sali A, Blundell T . Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol. 1993; 234(3):779-815. DOI: 10.1006/jmbi.1993.1626. View

18.

Pandit S, Skolnick J . Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score. BMC Bioinformatics. 2008; 9:531. PMC: 2628391. DOI: 10.1186/1471-2105-9-531. View

19.

Wang G, Dunbrack Jr R . Scoring profile-to-profile sequence alignments. Protein Sci. 2004; 13(6):1612-26. PMC: 2279992. DOI: 10.1110/ps.03601504. View

20.

Kirkpatrick S, Gelatt Jr C, Vecchi M . Optimization by simulated annealing. Science. 1983; 220(4598):671-80. DOI: 10.1126/science.220.4598.671. View