PATTERN-INDUCED MULTI-SEQUENCE ALIGNMENT (PIMA) ALGORITHM EMPLOYING SECONDARY STRUCTURE-DEPENDENT GAP PENALTIES FOR USE IN COMPARATIVE PROTEIN MODELING

被引：231
作者：
SMITH, RF [1 ]
SMITH, TF [1 ]
机构：
[1] HARVARD UNIV, DANA FARBER CANC INST, DEPT BIOSTAT, BOSTON, MA 02115 USA
来源：
PROTEIN ENGINEERING | 1992年 / 5卷 / 01期
关键词：
ALIGNMENTS; HOMOLOGY; MODELING; PROTEIN SEQUENCE; SECONDARY STRUCTURE;
D O I：
10.1093/protein/5.1.35
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
A multiple sequence alignment algorithm is described that uses a dynamic programming-based pattern construction method to align a set of homologous sequences based on their common pattern of conserved sequence elements. This pattern-induced multi-sequence alignment (PIMA) algorithm can employ secondary-structure dependent gap penalties for use in comparative modelling of new sequences when the three-dimensional structure of one or more members of the same family is known. We show that the use of secondary structure information can significantly improve the accuracy of aligning structure boundaries in a set of homologous sequences even when the structure of only one member of the family is known.
引用
收藏
页码：35 / 41
页数：7
相关论文
共 56 条
[1]   TREES, STARS, AND MULTIPLE BIOLOGICAL SEQUENCE ALIGNMENT [J].
ALTSCHUL, SF ;
LIPMAN, DJ .
SIAM JOURNAL ON APPLIED MATHEMATICS, 1989, 49 (01) :197-209
[2]   GAP COSTS FOR MULTIPLE SEQUENCE ALIGNMENT [J].
ALTSCHUL, SF .
JOURNAL OF THEORETICAL BIOLOGY, 1989, 138 (03) :297-309
[3]   BASIC LOCAL ALIGNMENT SEARCH TOOL [J].
ALTSCHUL, SF ;
GISH, W ;
MILLER, W ;
MYERS, EW ;
LIPMAN, DJ .
JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410
[4]   EVALUATION AND IMPROVEMENTS IN THE AUTOMATIC ALIGNMENT OF PROTEIN SEQUENCES [J].
BARTON, GJ ;
STERNBERG, MJE .
PROTEIN ENGINEERING, 1987, 1 (02) :89-94
[5]   FLEXIBLE PROTEIN-SEQUENCE PATTERNS - A SENSITIVE METHOD TO DETECT WEAK STRUCTURAL SIMILARITIES [J].
BARTON, GJ ;
STERNBERG, MJE .
JOURNAL OF MOLECULAR BIOLOGY, 1990, 212 (02) :389-402
[6]   A STRATEGY FOR THE RAPID MULTIPLE ALIGNMENT OF PROTEIN SEQUENCES - CONFIDENCE LEVELS FROM TERTIARY STRUCTURE COMPARISONS [J].
BARTON, GJ ;
STERNBERG, MJE .
JOURNAL OF MOLECULAR BIOLOGY, 1987, 198 (02) :327-337
[7]   DETERMINANTS OF A PROTEIN FOLD - UNIQUE FEATURES OF THE GLOBIN AMINO-ACID-SEQUENCES [J].
BASHFORD, D ;
CHOTHIA, C ;
LESK, AM .
JOURNAL OF MOLECULAR BIOLOGY, 1987, 196 (01) :199-216
[8]   KNOWLEDGE-BASED PREDICTION OF PROTEIN STRUCTURES AND THE DESIGN OF NOVEL MOLECULES [J].
BLUNDELL, TL ;
SIBANDA, BL ;
STERNBERG, MJE ;
THORNTON, JM .
NATURE, 1987, 326 (6111) :347-352
[9]   A METHOD TO IDENTIFY PROTEIN SEQUENCES THAT FOLD INTO A KNOWN 3-DIMENSIONAL STRUCTURE [J].
BOWIE, JU ;
LUTHY, R ;
EISENBERG, D .
SCIENCE, 1991, 253 (5016) :164-170
[10]   IDENTIFICATION OF PROTEIN FOLDS - MATCHING HYDROPHOBICITY PATTERNS OF SEQUENCE SETS WITH SOLVENT ACCESSIBILITY PATTERNS OF KNOWN STRUCTURES [J].
BOWIE, JU ;
CLARKE, ND ;
PABO, CO ;
SAUER, RT .
PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1990, 7 (03) :257-264
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