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Tuning interval branch-and-prune for protein structure determination. (English) Zbl 1422.92109
Summary: The interval branch and prune \(i\)BP algorithm for obtaining solutions to the interval discretizable molecular distance geometry problem \(i\)DMDGP has proven itself as a powerful method for molecular structure determination. However, substantial obstacles still must be overcome before \(i\)BP may be employed as a tractable general-purpose alternative to existing structure determination algorithms. This work introduces an iterative variant of the \(i\)BP algorithm that leverages existing knowledge of protein structures in order to reduce the size of the effective search space by many orders of magnitude. These improvements are included in a newly released implementation of the \(i\)BP software that aims to provide a solid platform for both research and application of the \(i\)DMDGP.

MSC:
92D20 Protein sequences, DNA sequences
92-08 Computational methods for problems pertaining to biology
Software:
ARIA; CHARMM; CNS; iBP; Xplor-NIH
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[1] Berkholz, DS; Driggers, CM; Shapovalov, MV; Dunbrack, RL; Karplus, PA, Nonplanar peptide bonds are common and conserved but not biased toward active sites, Proc. Natl. Acad. Sci. USA, 109, 449-453, (2012)
[2] Brooks, BR; Bruccoleri, RE; Olafson, BD; States, DJ; Swaminathan, S.; Karplus, M., CHARMM: a program for macromolecular energy, minimization, and dynamics calculations, J. Comput. Chem., 4, 187-217, (1983)
[3] Brünger, AT; Adams, PD; Clore, GM; DeLano, WL; Gros, P.; Grosse-Kunstleve, RW; Jiang, JS; Kuszewski, J.; Nilges, M.; Pannu, NS; Read, RJ; Rice, LM; Simonson, T.; Warren, GL, Crystallography and NMR system: a new software suite for macromolecular structure determination, Acta Cryst., D54, 905-921, (1998)
[4] Brünger, AT; Nilges, M., Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMR-spectroscopy, Q. Rev. Biophys., 26, 49-125, (1993)
[5] Cassioli, A.; Bardiaux, B.; Bouvier, G.; Mucherino, A.; Alves, R.; Liberti, L.; Nilges, M.; Lavor, C.; Malliavin, TE, An algorithm to enumerate all possible protein conformations verifying a set of distance constraints, BMC Bioinform., 16, 23-37, (2015)
[6] Cassioli, A.; Günlük, O.; Lavor, C.; Liberti, L., Discretization vertex orders in distance geometry, Discrete Appl. Math., 197, 27-41, (2015) · Zbl 1321.05029
[7] Costa, V.; Mucherino, A.; Lavor, C.; Cassioli, A.; Carvalho, LM; Maculan, N., Discretization orders for protein side chains, J. Glob. Optim., 60, 333-349, (2014) · Zbl 1312.90069
[8] Gil-Caballero, S.; Favier, A.; Brutscher, B., HNCA\(+\), HNCO\(+\), and HNCACB\(+\) experiments: improved performance by simultaneous detection of orthogonal coherence transfer pathways, J. Biomol. NMR, 60, 1-9, (2014)
[9] Goncalves, DS; Mucherino, A.; Lavor, C.; Liberti, L., Recent advances on the interval distance geometry problem, J. Glob. Optim., 63, 1-21, (2017) · Zbl 1382.90084
[10] Hinsen, K.; Hu, S.; Kneller, GR; Niemi, AJ, A comparison of reduced coordinate sets for describing protein structure, J. Chem. Phys, 139, 124,115, (2013)
[11] Ikura, M.; Kay, LE; Bax, A., A novel approach for sequential assignment of \(^1\)H, \(^{13}\)C and \(^{15}\)N spectra of proteins: heteronuclear triple-quantum resonance three-dimensional NMR spectroscopy. Application to calmodulin, Biochemistry, 15, 4659-4667, (1990)
[12] Lavor, C.; Alves, R.; Figueiredo, W.; Petraglia, A.; Maculan, N., Clifford algebra and the discretizable molecular distance geometry problem, Adv. Appl. Clifford Algebras, 25, 925-942, (2015) · Zbl 1327.15052
[13] Lavor, C.; Liberti, L.; Mucherino, A., The interval Branch-and-Prune algorithm for the discretizable molecular distance geometry problem with inexact distances, J. Glob. Optim., 56, 855-871, (2013) · Zbl 1272.90074
[14] Lescop, E.; Schanda, P.; Brutscher, B., A set of BEST triple-resonance experiments for time-optimized protein resonance assignment, J. Magn. Reson., 187, 163-169, (2007)
[15] Levitt, M.H.: Spin Dynamics: Basics of Nuclear Magnetic Resonance. Wiley, New York (2008)
[16] Liberti, L.; Lavor, C.; Maculan, N.; Mucherino, A., Euclidean distance geometry and applications, SIAM Rev., 56, 3-69, (2014) · Zbl 1292.51010
[17] Liberti, L., Lavor, C., Mucherino, A.: The Discretizable Molecular Distance Geometry Problem Seems Easier on Proteins, pp. 47-60. Springer, New York (2013) · Zbl 1366.92094
[18] Mucherino, A., Lavor, C., Liberti, L., Maculan, N.: Finding low-energy homopolymer conformations by a discrete approach. In: Global Optimization Workshop 2012, Natal (2012)
[19] Ramachandran, GN; Ramakrishnan, C.; Sasisekharan, V., Stereochemistry of polypeptide chain configurations, J. Mol. Biol., 7, 95-99, (1963)
[20] Rieping, W.; Habeck, M.; Bardiaux, B.; Bernard, A.; Malliavin, TE; Nilges, M., ARIA2: automated NOE assignment and data integration in NMR structure calculation, Bioinformatics, 23, 381-382, (2007)
[21] Rosato, A.; Vranken, W.; Fogh, RH; Ragan, TJ; Tejero, R.; Pederson, K.; Lee, HW; Prestegard, JH; Yee, A.; Wu, B.; Lemak, A.; Houliston, S.; Arrowsmith, CH; Kennedy, M.; Acton, TB; Xiao, R.; Liu, G.; Montelione, GT; Vuister, GW, The second round of critical assessment of automated structure determination of proteins by NMR: CASD-NMR-2013, J. Biomol. NMR, 62, 2728-2733, (2013)
[22] Schwieters, CD; Kuszewski, JJ; Tjandra, N.; Clore, GM, The Xplor-NIH NMR molecular structure determination package, J. Magn. Reson., 160, 66-74, (2003)
[23] Shen, Y.; Bax, A., Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks, J. Biomol. NMR, 56, 227-241, (2013)
[24] Thompson, HB, Calculation of cartesian coordinates and their derivatives from internal molecular coordinates, J. Chem. Phys., 47, 3407-3410, (1967)
[25] Vuister, GW; Bax, A., Quantitative J correlation: a new approach for measuring homonuclear three-bond \(J_{HN{H_\alpha }}\) coupling constants in \(^{15}\)N-enriched proteins, J. Am. Chem. Soc., 115, 7772-7777, (1993)
[26] Weiner, PK; Kollman, PA, AMBER: assisted model building with energy refinement. A general program for modeling molecules and their interactions, J. Comput. Chem., 2, 287-303, (1981)
[27] Wüthrich, K.: NMR of Proteins and Nucleic Acids. Wiley, New York (1986)
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