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An effective convergence independent loop closure method using Forward-Backward Cyclic Coordinate Descent

Authors:

Jing HeAuthors Info & Claims

International Journal of Data Mining and Bioinformatics, Volume 3, Issue 3

Pages 346 - 361

https://doi.org/10.1504/IJDMB.2009.026712

Published: 01 June 2009 Publication History

Abstract

Cyclic Coordinate Descent (CCD) is a popular robotic approach to generate a possible loop that closes the gap between two constrained portions of a protein chain (Canutescu and Dunbrack 2003). In this paper, we describe an effective Forward-Backward CCD (FBCCD) method to connect the two constrained portions of a protein chain without requiring the loop to converge. A test of 30 loops of length 4, 8 and 12 suggests that our method takes fewer number of cycles to produce loops of comparable accuracy and more accurate second portion of the chain, when it is compared to the CCD method.

References

[1]

Baker, D. and Sali, A. (2001) 'Protein structure prediction and structural genomics', Science, Vol. 294, pp.93-96.

[2]

Boomsma, W. and Hamelryck, T. (2005) 'Full cyclic coordinate descent: solving the protein loop closure problem in C¿ space', BMC Bioinformatics, Vol. 6, p.159.

[3]

Bruccoleri, R.E. and Karplus, M. (1987) 'Prediction of the folding of short polypeptide segments by uniform conformational sampling', Biopolymers, Vol. 26, pp.137-168.

[4]

Canutescu, A.A. and Dunbrack, R.L.J. (2003) 'Cyclic coordinate descent: a robotics algorithm for protein loop closure', Protein Sci., Vol. 12, pp.963-972.

[5]

Coutsias, E.A., Seok, C., Jacobson, M.P. and Dill, K.A. (2004) 'A kinematic view of loop closure', J. Comput. Chem., Vol. 25, pp.510-528.

[6]

Craig, J.J. (1989) Introduction to Robotics: Manipulation and Control, 2nd ed., Addison-Wesley, MA, USA.

[7]

Deane, C. and Blundell, T. (2001) 'CODA: a combined algorithm for predicting the structurally variable regions of protein models', Protein Sci., Vol. 10, pp.599-612.

[8]

Fidelis, K., Stern, P., Bacon, D. and Moult, J. (1994) 'Comparison of systematic search and database methods for constructing segments of protein structure', Protein Eng., Vol. 7, pp.953-960.

[9]

Fine, R.M., Wang, H., Shenkin, P.S., Yarmush, D.L. and Levinthal, C. (1986) 'Predicting antibody hypervariable loop conformations, II minimization and molecular dynamics studies of mcp603 from many randomly generated loop conformations', Proteins, Vol. 1, pp.342-362.

[10]

Ginalski, K. (2006) 'Comparative modeling for protein structure prediction', Current Opinion in Structural Biology, Vol. 16, pp.172-177.

[11]

Go, N. and Scheraga, H.A. (1970) Ring closure and local conformational deformations of chain molecules. Macromolecules, Vol. 3, pp.178-186.

[12]

He, J. and Al-Nasr, K. (2007) 'An approximate robotics algorithm to assemble a loop between two helices', IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBM), pp.74-79.

[13]

Jacobson, M., Pincus, D., Rapp, C., Day, T., Honig, B., Shaw, D. and Friesner, R. (2004) 'A hierarchical approach to all-atom protein loop prediction', Proteins, Vol. 55, pp.351-367.

[14]

Jiang, H. and Blouin, C. (2006) 'Ab initio construction of all-atom loop conformations', Journal of Molecular Modeling, Vol. 12, No. 2, pp.221-228.

[15]

John, B., Sali, A. and Journals, O. (2003) 'Comparative protein structure modeling by iterative alignment, model building and model assessment', Nucleic Acids Research, Vol. 31, pp.3982-3992.

[16]

Kolodny, R., Guibas, L., Levitt, M. and Koehl, P. (2005) 'Inverse kinematics in biology: the protein loop closure problem', International Journal of Robotics Research, Vol. 24, p.151.

[17]

Li, W., Liu, Z. and Lai, L. (1999) 'Exploring the conformational diversity of loops on conserved frameworks', Biopolymers, Vol. 49, pp.481-495.

[18]

Manocha, D. and Canny, J. (1994) 'Efficient inverse kinematics for general 6R manipulator', IEEE Trans. Robot. Autom., Vol. 10, pp.648-657.

[19]

Manocha, D. and Zhu, Y. (1994) 'Kinematic manipulation of molecular chains subject to rigid constraints', Proc. Int. Conf. Intell. Syst. Mol. Biol., Stanford, CA, pp.285-293.

[20]

Manocha, D., Zhu, Y. and Wright, W. (1995) 'Conformational analysis of molecular chains using nano-kinematics', Comput. Appl. Biosci., Vol. 11, pp.71-86.

[21]

Moult, J. and James, M.N.G. (1986) 'An algorithm for determining the conformation of polypeptide segments in proteins by systematic search', Proteins, Vol. 1, pp.146-163.

[22]

Palmer, K.A. and Scheraga, H.J. (1991) 'Standard-geometry chains fitted to x-ray derived structures: validation of the rigid-geometry approximation, I. Chain closure through a limited search of loop conformations', Journal Computational Chemistry, Vol. 2, pp.505-526.

Digital Library

[23]

Raghavan, M. and Roth, B. (1991) 'Kinematic analysis of the 6r manipulator of general geometry', Proc. The Fifth International Symposium on Robotics Research, Tokyo, pp.263-269.

[24]

Rapp, C. and Friesner, R. (1999) 'Prediction of loop geometries using a generalised born model of solvation effects', Proteins, Vol. 35, pp.173-183.

[25]

Ring, C.S., Kneller, D.G., Langridge, R. and Cohen, F.E. (1992) 'Taxonomy and conformational analysis of loops in proteins', J. Mol. Biol., Vol. 224, pp.685-699.

[26]

Shehu, A., Clementi, C. and Kavraki, L.E. (2006) 'Modeling protein conformational ensembles: from missing loops to equilibrium fluctuations', Proteins: Structures, Functions and Bioinformatics, Vol. 65, pp.164-179.

[27]

Shenkin, P.S., Yarmush, D.L., Fine, R.M., Wang, H.J. and Levinthal, C. (1987) 'Predicting antibody hypervariable loop conformation, I. ensembles of random conformations for ring-like structure', Biopolymers, Vol. 26, pp.2053-2085.

[28]

Soto, C., Fasnacht, M., Zhu, J., Forrest, L. and Honig, B. (2007) 'Loop modeling: sampling, filtering, and scoring', Proteins: Structures, Functions, and Bioinformatics, Vol. 70, pp.834-843.

[29]

Tosatto, S., Bindewald, E., Hesser, J. and Manner, R. (2002) 'A divide and conquer approach to fast loop modeling', Protein Eng., Vol. 15, pp.279-286.

[30]

Tress, M., Ezkurdia, I., Grana, O., López, G. and Valencia, A. (2005) 'Assessment of predictions submitted for the CASP6 comparative modeling category', PROTEINS: Structure, Function, and Bioinformatics, Vol. 7, pp.27-45.

[31]

Vlijmen, H.v. and Karplus, M. (1997) 'PDB-based protein loop prediction: parameters for selection and methods for optimisation', J. Mol. Biol., Vol. 267, pp.975-1001.

[32]

Wang, C., Bradley, P. and Baker, D. (2007) 'Protein-protein docking with backbone flexibility', J. Mol. Biol., Vol. 373, pp.503-519.

[33]

Wedemeyer, W.J. and Scheraga, H.A. (1999) 'Exact analytical loop closure in proteins using polynomial equations', J. Comput. Chem., Vol. 20, pp.819-844.

[34]

Wojcik, J., Mornon, J. and Chomilier, J. (1999) 'New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification', J. Mol. Biol., Vol. 289, pp.1469-1490.

[35]

Xiang, Z. (2006) 'Advances in homology protein structure modeling', Curr. Prot. Pept. Sci., Vol. 7, pp.217-227.

[36]

Xiang, Z., Soto, C. and Honig, B. (2002) 'Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction', Proc. Natl. Acad. Sci., USA, pp.7432-7437.

[37]

Zhang, M., White, R.A., Wang, L., Goldman, R., Kavraki, L. and Hassett, B. (2005) 'Improving conformational searches by geometric screening', Bioinformatics, Vol. 21, pp.624-630.

Digital Library

[38]

Zheng, Q. and Kyle, D. (1996) 'Accuracy and reliability of the scaling-relaxation method for loop closure: an evaluation based on extensive and multiple copy conformational samplings', Proteins, Vol. 24, pp.209-217.

Cited By

Manavi KTashakkori STapia LHaspel NCowen LShehu AKahveci TPozzi G(2017)Gaussian Mixture Models with Constrained Flexibility for Fitting Tomographic Tilt SeriesProceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics10.1145/3107411.3107504(710-715)Online publication date: 20-Aug-2017
https://dl.acm.org/doi/10.1145/3107411.3107504
Nasr KHe JBaldi PWang W(2014)Construction of protein backbone pieces using segment-based FBCCD and Cryo-EM skeletonProceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics10.1145/2649387.2660838(711-716)Online publication date: 20-Sep-2014
https://dl.acm.org/doi/10.1145/2649387.2660838
Al Nasr KChen LSi DRanjan DZubair MHe JRanka SKahveci TSingh M(2012)Building the initial chain of the proteins through de novo modeling of the cryo-electron microscopy volume data at the medium resolutionsProceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine10.1145/2382936.2382999(490-497)Online publication date: 7-Oct-2012
https://dl.acm.org/doi/10.1145/2382936.2382999

An effective convergence independent loop closure method using Forward-Backward Cyclic Coordinate Descent
1. Applied computing
  1. Life and medical sciences

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Published In

cover image International Journal of Data Mining and Bioinformatics

International Journal of Data Mining and Bioinformatics Volume 3, Issue 3

June 2009

133 pages

ISSN:1748-5673

EISSN:1748-5681

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Inderscience Publishers

Geneva 15, Switzerland

Publication History

Published: 01 June 2009

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Cited By

Manavi KTashakkori STapia LHaspel NCowen LShehu AKahveci TPozzi G(2017)Gaussian Mixture Models with Constrained Flexibility for Fitting Tomographic Tilt SeriesProceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics10.1145/3107411.3107504(710-715)Online publication date: 20-Aug-2017
https://dl.acm.org/doi/10.1145/3107411.3107504
Nasr KHe JBaldi PWang W(2014)Construction of protein backbone pieces using segment-based FBCCD and Cryo-EM skeletonProceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics10.1145/2649387.2660838(711-716)Online publication date: 20-Sep-2014
https://dl.acm.org/doi/10.1145/2649387.2660838
Al Nasr KChen LSi DRanjan DZubair MHe JRanka SKahveci TSingh M(2012)Building the initial chain of the proteins through de novo modeling of the cryo-electron microscopy volume data at the medium resolutionsProceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine10.1145/2382936.2382999(490-497)Online publication date: 7-Oct-2012
https://dl.acm.org/doi/10.1145/2382936.2382999

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