Algorithms, applications, and challenges of protein structure alignment

Advances in Protein Chemistry and Structural Biology

Volumn 94, Issue , 2014, Pages 121-175

  Ma, Jianzhu ^a   Wang, Sheng ^a  

^a TOYOTA TECHNOLOGICAL INSTITUTE AT CHICAGO   (United States)

Author keywords

Multiple protein structure alignment; Pairwise protein structure alignment; Protein structural alphabet; Protein structure; Structural alphabet substitution matrix

Indexed keywords

ALGORITHM; ARTICLE; GENETIC CONSERVATION; HUMAN; MEDICAL INFORMATICS; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN STRUCTURE; STRUCTURAL BIOINFORMATICS; AMINO ACID SEQUENCE; CHEMISTRY; MOLECULAR GENETICS; PROTEIN CONFORMATION; SEQUENCE ALIGNMENT;

PROTEIN;

ALGORITHMS; AMINO ACID SEQUENCE; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEINS; SEQUENCE ALIGNMENT;

EID: 84896279116     PISSN: 18761623     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-800168-4.00005-6     Document Type: Chapter

References (111)

1. Altschul S., Madden T., Schaffer A., Zhang J., Zhang Z., Miller W., et al. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research 1997, 25(17):3389.
2. Andersen J.N., Mortensen O.H., Peters G.H., Drake P.G., Iversen L.F., Olsen O.H., et al. Structural and evolutionary relationships among protein tyrosine phosphatase domains. Molecular and Cellular Biology 2001, 21(21):7117-7136.
3. Birzele F., Gewehr J.E., Csaba G., Zimmer R. Vorolign-Fast structural alignment using Voronoi contacts. Bioinformatics 2007, 23(2):e205-e211. 23/2/e205 [pii]. 10.1093/bioinformatics/btl294.
4. Bornot A., Etchebest C., De Brevern A.G. A new prediction strategy for long local protein structures using an original description. Proteins: Structure, Function, and Bioinformatics 2009, 76(3):570-587.
5. Bradley P., Kim P.S., Berger B. TRILOGY: Discovery of sequence-structure patterns across diverse proteins 2002.
6. Brylinski M., Skolnick J. A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proceedings of the National Academy of Sciences 2008, 105(1):129-134.
7. Budowski-Tal I., Nov Y., Kolodny R. FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately. Proceedings of the National Academy of Sciences 2010, 107(8):3481-3486.
8. Bystroff C., Baker D. Prediction of local structure in proteins using a library of sequence-structure motifs. Journal of Molecular Biology 1998, 281(3):565-577.
9. Camproux A., Tuffery P., Chevrolat J., Boisvieux J., Hazout S. Hidden Markov model approach for identifying the modular framework of the protein backbone. Protein Engineering 1999, 12(12):1063-1073.
10. Carpentier M., Brouillet S., Pothier J. YAKUSA: A fast structural database scanning method. Proteins: Structure, Function, and Bioinformatics 2005, 61(1):137-151.
11. Cheng H., Kim B.H., Grishin N.V. MALIDUP: A database of manually constructed structure alignments for duplicated domain pairs. Proteins: Structure, Function, and Bioinformatics 2008, 70(4):1162-1166.
12. Cheng H., Kim B.H., Grishin N.V. MALISAM: A database of structurally analogous motifs in proteins. Nucleic Acids Research 2008, 36(Suppl. 1):D211.
13. Csaba G., Birzele F., Zimmer R. Protein structure alignment considering phenotypic plasticity. Bioinformatics 2008, 24(16):i98-i104.
14. Daniluk P., Lesyng B. A novel method to compare protein structures using local descriptors. BMC Bioinformatics 2011, 12(1):344.
15. Dayhoff M.O., Schwartz R.M. A model of evolutionary change in proteins 1978.
16. De Brevern A., Etchebest C., Hazout S. Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. Proteins: Structure, Function, and Bioinformatics 2000, 41(3):271-287.
17. de Brevern A.G., Valadié H., Hazout S., Etchebest C. Extension of a local backbone description using a structural alphabet: A new approach to the sequence-structure relationship. Protein Science 2002, 11(12):2871-2886.
18. De Brevern A., Wong H., Tournamille C., Colin Y., Le Van Kim C., Etchebest C. A structural model of a seven-transmembrane helix receptor: The Duffy antigen/receptor for chemokine (DARC). Biochimica et Biophysica Acta (BBA) General Subjects 2005, 1724(3):288-306.
19. Dror O., Benyamini H., Nussinov R., Wolfson H. MASS: Multiple structural alignment by secondary structures. Bioinformatics 2003, 19(Suppl. 1):i95-i104.
20. Dudev M., Lim C. Discovering structural motifs using a structural alphabet: Application to magnesium-binding sites. BMC Bioinformatics 2007, 8(1):106.
21. Dunbrack R.L. Sequence comparison and protein structure prediction. Current Opinion in Structural Biology 2006, 16(3):374-384.
22. Edgar R.C., Batzoglou S. Multiple sequence alignment. Current Opinion in Structural Biology 2006, 16(3):368-373.
23. Eidhammer I., Jonassen I., Taylor W.R. Structure comparison and structure patterns. Journal of Computational Biology 2000, 7(5):685-716.
24. Emekli U., Schneidman-Duhovny D., Wolfson H.J., Nussinov R., Haliloglu T. HingeProt: Automated prediction of hinges in protein structures. Proteins: Structure, Function, and Bioinformatics 2008, 70(4):1219-1227.
25. Etchebest C., Benros C., Bornot A., Camproux A.-C., de Brevern A. A reduced amino acid alphabet for understanding and designing protein adaptation to mutation. European Biophysics Journal 2007, 36(8):1059-1069.
26. Flocco M.M., Mowbray S.L. Cα-based torsion angles: A simple tool to analyze protein conformational changes. Protein Science 1995, 4(10):2118-2122.
27. Fourrier L., Benros C., De Brevern A.G. Use of a structural alphabet for analysis of short loops connecting repetitive structures. BMC Bioinformatics 2004, 5(1):58.
28. Gibrat J., Madej T., Spouge J., Bryant S. The VAST protein structure comparison method. Biophysical Journal 1997, 72:298.
29. Guda C., Lu S., Scheeff E.D., Bourne P.E., Shindyalov I.N. CE-MC: A multiple protein structure alignment server. Nucleic Acids Research 2004, 32(Suppl. 2):W100.
30. Harder T., Borg M., Boomsma W., Røgen P., Hamelryck T. Fast large-scale clustering of protein structures using Gauss integrals. Bioinformatics 2012, 28(4):510-515.
31. Hasegawa H., Holm L. Advances and pitfalls of protein structural alignment. Current Opinion in Structural Biology 2009, 19(3):341-348.
32. Henikoff S., Henikoff J.G. Amino acid substitution matrices from protein blocks. Proceedings of the National Academy of Sciences 1992, 89(22):10915-10919.
33. Holm L., Rosenström P. Dali server: Conservation mapping in 3D. Nucleic Acids Research 2010, 38(Suppl. 2):W545-W549.
34. Holm L., Sander C. Protein structure comparison by alignment of distance matrices. Journal of Molecular Biology 1993, 233:123.
35. Holm L., Sander C. The FSSP database of structurally aligned protein fold families. Nucleic Acids Research 1994, 22(17):3600.
36. Ilinkin I., Ye J., Janardan R. Multiple structure alignment and consensus identification for proteins. BMC Bioinformatics 2010, 11:71. 1471-2105-11-71 [pii]. 10.1186/1471-2105-11-71.
37. Irving J.A., Whisstock J.C., Lesk A.M. Protein structural alignments and functional genomics. Proteins: Structure, Function, and Bioinformatics 2001, 42(3):378-382.
38. Joseph A.P., Agarwal G., Mahajan S., Gelly J.-C., Swapna L.S., Offmann B., et al. A short survey on protein blocks. Biophysical Reviews 2010, 2(3):137-145.
39. Joseph A.P., Bornot A., de Brevern A.G. Local structure alphabets. Introduction to protein structure prediction: Methods and algorithms 2010, 75-106. John Wiley & Sons, Inc., Hoboken, New Jersey. H. Rangwala, G. Karypis (Eds.).
40. Jung J., Lee B. Protein structure alignment using environmental profiles. Protein Engineering 2000, 13(8):535-543.
41. Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta Crystallographica. Section A: Crystal Physics, Diffraction, Theoretical and General Crystallography 1976, 32(5):922-923.
42. Källberg M., Wang H., Wang S., Peng J., Wang Z., Lu H., et al. Template-based protein structure modeling using the RaptorX web server. Nature Protocols 2012, 7(8):1511-1522.
43. Kawabata T. MATRAS: A program for protein 3D structure comparison. Nucleic Acids Research 2003, 31(13):3367.
44. Kim C., Lee B. Accuracy of structure-based sequence alignment of automatic methods. BMC Bioinformatics 2007, 8(1):355.
45. Kim C., Tai C.H., Lee B. Iterative refinement of structure-based sequence alignments by seed extension. BMC Bioinformatics 2009, 10(1):210.
46. Koehl P. Protein structure classification. Reviews in Computational Chemistry 2006, 22:1.
47. Kolbeck B., May P., Schmidt-Goenner T., Steinke T., Knapp E.-W. Connectivity independent protein-structure alignment: A hierarchical approach. BMC Bioinformatics 2006, 7(1):510.
48. Kolodny R., Koehl P., Guibas L., Levitt M. Small libraries of protein fragments model native protein structures accurately. Journal of Molecular Biology 2002, 323(2):297-307.
49. Konagurthu A.S., Whisstock J.C., Stuckey P.J., Lesk A.M. MUSTANG: A multiple structural alignment algorithm. Proteins: Structure, Function, and Bioinformatics 2006, 64(3):559-574.
50. Krissinel E., Henrick K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallographica. Section D: Biological Crystallography 2004, 60(12):2256-2268.
51. Lackner P., Koppensteiner W.A., Sippl M.J., Domingues F.S. ProSup: A refined tool for protein structure alignment. Protein Engineering 2000, 13(11):745.
52. Lafferty J., McCallum A., Pereira F. Conditional random fields: Probabilistic models for segmenting and labeling sequence data 2001, (pp. 282-289)., Morgan Kaufmann Publishers Inc., San Francisco, CA, USA.
53. Le Q., Pollastri G., Koehl P. Structural alphabets for protein structure classification: A comparison study. Journal of Molecular Biology 2009, 387(2):431-450.
54. Levitt M., Gerstein M. A unified statistical framework for sequence comparison and structure comparison. Proceedings of the National Academy of Sciences 1998, 95(11):5913.
55. Lupyan D., Leo-Macias A., Ortiz A.R. A new progressive-iterative algorithm for multiple structure alignment. Bioinformatics 2005, 21(15):3255.
56. Ma J., Peng J., Wang S., Xu J. A conditional neural fields model for protein threading. Bioinformatics 2012, 28(12):i59-i66.
57. Ma J., Peng J., Wang S., Xu J. Estimating the partition function of graphical models using Langevin importance sampling. JMLR W&CP 2013, 31:433-441.
58. Ma J., Wang S., Zhao F., Xu J. Protein threading using context-specific alignment potential. Bioinformatics 2013, 29(13):i257-i265.
59. Marchler-Bauer A., Anderson J.B., Cherukuri P.F., DeWeese-Scott C., Geer L.Y., Gwadz M., et al. CDD: A conserved domain database for protein classification. Nucleic Acids Research 2005, 33(Suppl. 1):D192.
60. Matsuda H., Taniguchi F., Hashimoto A. An approach to detection of protein structural motifs using an encoding scheme of backbone conformation 1997.
61. McCammon J.A. Dynamics of folded proteins. Nature 1977, 267:16.
62. Menke M., Berger B., Cowen L. Matt: Local flexibility aids protein multiple structure alignment. PLoS Computational Biology 2008, 4(1):e10.
63. Micheletti C., Orland H. MISTRAL: A tool for energy-based multiple structural alignment of proteins. Bioinformatics 2009, 25(20):2663-2669.
64. Mizuguchi K., Deane C.M., Blundell T.L., Overington J.P. HOMSTRAD: A database of protein structure alignments for homologous families. Protein Sciences 1998, 7(11):2469-2471. 10.1002/pro.5560071126.
65. Mosca R., Brannetti B., Schneider T. Alignment of protein structures in the presence of domain motions. BMC Bioinformatics 2008, 9(1):352.
66. Murzin A., Brenner S., Hubbard T., Chothia C. SCOP: A structural classification of proteins database for the investigation of sequences and structures. Journal of Molecular Biology 1995, 247(4):536-540.
67. Nadimpalli S., Daniels N., Cowen L. Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment. BMC Bioinformatics 2012, 13:259.
68. Orengo C.A., Michie A., Jones S., Jones D.T., Swindells M., Thornton J.M. CATH-A hierarchic classification of protein domain structures. Structure 1997, 5(8):1093-1109.
69. Ortiz A.R., Strauss C.E., Olmea O. MAMMOTH (matching molecular models obtained from theory): An automated method for model comparison. Protein Science 2002, 11(11):2606-2621.
70. Panchenko A., Marchler-Bauer A., Bryant S.H. Threading with explicit models for evolutionary conservation of structure and sequence. Proteins: Structure, Function, and Bioinformatics 1999, 37(S3):133-140.
71. Pandini A., Fornili A., Kleinjung J. Structural alphabets derived from attractors in conformational space. BMC Bioinformatics 2010, 11(1):97.
72. Park B.H., Levitt M. The complexity and accuracy of discrete state models of protein structure. Journal of Molecular Biology 1995, 249(2):493-507.
73. Pauling L., Corey R.B., Branson H.R. The structure of proteins: Two hydrogen-bonded helical configurations of the polypeptide chain. Proceedings of the National Academy of Sciences 1951, 37(4):205-211.
74. Peng J., Bo L., Xu J. Conditional neural fields 2009.
75. Peng J., Xu J. A multiple-Template approach to protein threading. Proteins: Structure, Function, and Bioinformatics 2011, 79(6):1930-1939.
76. Potestio R., Aleksiev T., Pontiggia F., Cozzini S., Micheletti C. ALADYN: A web server for aligning proteins by matching their large-scale motion. Nucleic Acids Research 2010, 38(Suppl. 2):W41-W45.
77. Robson B., Pain R.H. Analysis of the code relating sequence to conformation in globular proteins. Development of a stereochemical alphabet on the basis of intra-residue information. Biochemistry Journal 1974, 141:869-882.
78. Rooman M.J., Kocher J.-P.A., Wodak S.J. Prediction of protein backbone conformation based on seven structure assignments: Influence of local interactions. Journal of Molecular Biology 1991, 221(3):961-979.
79. Roy A., Yang J., Zhang Y. COFACTOR: An accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Research 2012, 40(W1):W471-W477.
80. Sadowski M.I., Taylor W.R. Evolutionary inaccuracy of pairwise structural alignments. Bioinformatics 2012, 28(9):1209-1215.
81. Shao M., Wang S., Wang C., Yuan X., Li S., Zheng W., et al. Incorporating ab initio energy into threading approaches for protein structure prediction. BMC Bioinformatics 2011, 12(Suppl. 1):S54.
82. Shapiro J., Brutlag D. FoldMiner and LOCK 2: Protein structure comparison and motif discovery on the web. Nucleic Acids Research 2004, 32(Suppl. 2):W536.
83. Shatsky M., Nussinov R., Wolfson H.J. Flexible protein alignment and hinge detection. Proteins: Structure, Function, and Bioinformatics 2002, 48(2):242-256.
84. Shatsky M., Nussinov R., Wolfson H.J. A method for simultaneous alignment of multiple protein structures. Proteins 2004, 56(1):143-156. 10.1002/prot.10628.
85. Shindyalov I.N., Bourne P.E. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Engineering 1998, 11(9):739.
86. Sippl M.J., Wiederstein M. Detection of spatial correlations in protein structures and molecular complexes. Structure 2012, 20(4):718-728.
87. Slater A.W., Castellanos J.I., Sippl M.J., Melo F. Towards the development of standardized methods for comparison, ranking and evaluation of structure alignments. Bioinformatics 2013, 29(1):47-53.
88. Taylor W.R., Orengo C.A. Protein structure alignment. Journal of Molecular Biology 1989, 208(1):1-22.
89. Tung C.-H., Huang J.-W., Yang J.-M. Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database. Genome Biology 2007, 8(3):R31.
90. Tyagi M., De Brevern A., Srinivasan N., Offmann B. Protein structure mining using a structural alphabet. Proteins: Structure, Function, and Bioinformatics 2008, 71(2):920-937.
91. Van Walle I., Lasters I., Wyns L. SABmark-A benchmark for sequence alignment that covers the entire known fold space. Bioinformatics 2005, 21(7):1267-1268. bth493 [pii]. 10.1093/bioinformatics/bth493.
92. Wang S. CLeFAPS: Fast flexible alignment of protein structures based on conformational letters 2009, arXiv, preprint arXiv:0903.0582.
93. Wang S. Hydropathy conformational letter and its substitution matrix HP-CLESUM: An application to protein structural alignment 2010, arXiv, preprint arXiv:1001.2879.
94. Wang S., Ma J., Peng J., Xu J. Protein structure alignment beyond spatial proximity. Scientific Reports 2013, 3:1448.
95. Wang S., Peng J., Xu J. Alignment of distantly related protein structures: Algorithm, bound and implications to homology modeling. Bioinformatics 2011, 27(18):2537-2545.
96. Wang Z., Xu J. Predicting protein contact map using evolutionary and physical constraints by integer programming. Bioinformatics 2013, 29(13):i266-i273.
97. Wang S., Zheng W.M. CLePAPS: Fast pair alignment of protein structures based on conformational letters. Journal of Bioinformatics and Computational Biology 2008, 6(2):347-366. [pii]. 10.1142/S0219720008003461.
98. Wang S., Zheng W.M. Fast multiple alignment of protein structures using conformational letter blocks. Open Bioinformatics Journal 2009, 3:69-83.
99. Wass M.N., Kelley L.A., Sternberg M.J. 3DLigandSite: Predicting ligand-binding sites using similar structures. Nucleic Acids Research 2010, 38(Suppl. 2):W469-W473.
100. Xu J., Zhang Y. How significant is a protein structure similarity with TM-score=0.5?. Bioinformatics 2010, 26(7):889-895.
101. Yang L., Song G., Jernigan R.L. Protein elastic network models and the ranges of cooperativity. Proceedings of the National Academy of Sciences 2009, 106(30):12347-12352.
102. Yang Y., Zhan J., Zhao H., Zhou Y. A new size-independent score for pairwise protein structure alignment and its application to structure classification and nucleic-acid binding prediction. Proteins: Structure, Function, and Bioinformatics 2012, 80(8):2080-2088.
103. Ye Y., Godzik A. Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics 2003, 19(Suppl. 2):ii246-ii255.
104. Ye Y., Godzik A. Multiple flexible structure alignment using partial order graphs. Bioinformatics 2005, 21(10):2362.
105. Zemla A. LGA: A method for finding 3D similarities in protein structures. Nucleic Acids Research 2003, 31(13):3370-3374.
106. Zhang Y., Skolnick J. Scoring function for automated assessment of protein structure template quality. Proteins 2004, 57:702-710.
107. Zhang Y., Skolnick J. TM-align: A protein structure alignment algorithm based on the TM-score. Nucleic Acids Research 2005, 33(7):2302.
108. Zhao F., Xu J. A position-specific distance-dependent statistical potential for protein structure and functional study. Structure 2012, 20(6):1118-1126.
109. Zheng W. Protein conformational alphabets. Protein conformation: New research 2008, 1-49. Nova Science Publishers, Inc., New York. L.B. Roswell (Ed.).
110. Zheng W.M., Liu X. A protein structural alphabet and its substitution matrix CLESUM. Transactions on computational systems biology II 2005, 59-67. Springer, Berlin. S. Istrail, P. Pevzner, M. Waterman (Eds.).
111. Zhu J., Weng Z. FAST: A novel protein structure alignment algorithm. Proteins: Structure, Function, and Bioinformatics 2005, 58(3):618-627.