An iterative structure-assisted approach to sequence alignment and comparative modeling

David F. Burke; Charlotte M. Deane; Hampapathalu A. Nagarajaram; Nuria Campillo; Mercedes Martin-Martinez; Joaquim Mendes; Franck Molina; Jeff Perry; B. V.B. Reddy; Claudio M. Soares; Robert E. Steward; Mark Williams; Maria Armenia Carrondo; Tom L. Blundell; Kenji Mizuguchi

doi:10.1002/(SICI)1097-0134(1999)37:3+<55::AID-PROT8>3.0.CO;2-B

An iterative structure-assisted approach to sequence alignment and comparative modeling

David F. Burke, Charlotte M. Deane, Hampapathalu A. Nagarajaram, Nuria Campillo, Mercedes Martin-Martinez, Joaquim Mendes, Franck Molina, Jeff Perry, B. V.B. Reddy, Claudio M. Soares, Robert E. Steward, Mark Williams, Maria Armenia Carrondo, Tom L. Blundell, Kenji Mizuguchi^*

^*Corresponding author for this work

Centre for Host Microbiome Interactions

Research output: Contribution to journal › Article › peer-review

40 Citations (Scopus)

Abstract

Correct alignment of the sequence of a target protein with those of homologues of known three-dimensional structure is a key step in comparative modeling. Usually an iterative approach that takes account of the local and overall structural features is required. We describe such an approach that exploits databases of structural alignments of homologous proteins (HOMSTRAD, http://www-cryst.bioc.cam.ac.uk/homstrad) and protein superfamilies (CAMPASS, http://www-cryst.bioc.cam.ac.uk/campass), in which structure-based alignments are analyzed and formatted with the program JOY (http://www- cryst.bioc.cam.ac.uk/joy) to reveal conserved local structural features. The databases facilitate the recognition of a family or superfamily, they assist in the selection of useful parent structures, they are helpful in alignment of the target sequences with the parent set, and are useful for deriving relationships that can be used in validating models. In the iterative approach, a model is constructed on the basis of the proposed sequence alignment and this is then reexpressed in the JOY format and realigned with the parent set. This is repeated until the model and sequence alignment is optimized. We examine the case for comparison and use of multiple structures of family members, rather than a single parent structure. We use the targets attempted by our group in CASP3 to assess the value of such procedures.

Original language	English
Pages (from-to)	55-60
Number of pages	6
Journal	Proteins: Structure, Function and Genetics
Volume	37
Issue number	SUPPL. 3
DOIs	https://doi.org/10.1002/(SICI)1097-0134(1999)37:3+<55::AID-PROT8>3.0.CO;2-B
Publication status	Published - 1999

Keywords

Alignment annotation
Alignment databases
Local structural features
Loop modeling
Model evaluation
Protein family
Protein structure
Side-chain modeling
Structure prediction

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10.1002/(SICI)1097-0134(1999)37:3+<55::AID-PROT8>3.0.CO;2-B

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Burke, D. F., Deane, C. M., Nagarajaram, H. A., Campillo, N., Martin-Martinez, M., Mendes, J., Molina, F., Perry, J., Reddy, B. V. B., Soares, C. M., Steward, R. E., Williams, M., Carrondo, M. A., Blundell, T. L., & Mizuguchi, K. (1999). An iterative structure-assisted approach to sequence alignment and comparative modeling. Proteins: Structure, Function and Genetics, 37(SUPPL. 3), 55-60. https://doi.org/10.1002/(SICI)1097-0134(1999)37:3+<55::AID-PROT8>3.0.CO;2-B

@article{f3bb22bbf7bf4dd18c1525df1b22efbd,

title = "An iterative structure-assisted approach to sequence alignment and comparative modeling",

abstract = "Correct alignment of the sequence of a target protein with those of homologues of known three-dimensional structure is a key step in comparative modeling. Usually an iterative approach that takes account of the local and overall structural features is required. We describe such an approach that exploits databases of structural alignments of homologous proteins (HOMSTRAD, http://www-cryst.bioc.cam.ac.uk/homstrad) and protein superfamilies (CAMPASS, http://www-cryst.bioc.cam.ac.uk/campass), in which structure-based alignments are analyzed and formatted with the program JOY (http://www- cryst.bioc.cam.ac.uk/joy) to reveal conserved local structural features. The databases facilitate the recognition of a family or superfamily, they assist in the selection of useful parent structures, they are helpful in alignment of the target sequences with the parent set, and are useful for deriving relationships that can be used in validating models. In the iterative approach, a model is constructed on the basis of the proposed sequence alignment and this is then reexpressed in the JOY format and realigned with the parent set. This is repeated until the model and sequence alignment is optimized. We examine the case for comparison and use of multiple structures of family members, rather than a single parent structure. We use the targets attempted by our group in CASP3 to assess the value of such procedures.",

keywords = "Alignment annotation, Alignment databases, Local structural features, Loop modeling, Model evaluation, Protein family, Protein structure, Side-chain modeling, Structure prediction",

author = "Burke, {David F.} and Deane, {Charlotte M.} and Nagarajaram, {Hampapathalu A.} and Nuria Campillo and Mercedes Martin-Martinez and Joaquim Mendes and Franck Molina and Jeff Perry and Reddy, {B. V.B.} and Soares, {Claudio M.} and Steward, {Robert E.} and Mark Williams and Carrondo, {Maria Armenia} and Blundell, {Tom L.} and Kenji Mizuguchi",

year = "1999",

doi = "10.1002/(SICI)1097-0134(1999)37:3+<55::AID-PROT8>3.0.CO;2-B",

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Burke, DF, Deane, CM, Nagarajaram, HA, Campillo, N, Martin-Martinez, M, Mendes, J, Molina, F, Perry, J, Reddy, BVB, Soares, CM, Steward, RE, Williams, M, Carrondo, MA, Blundell, TL & Mizuguchi, K 1999, 'An iterative structure-assisted approach to sequence alignment and comparative modeling', Proteins: Structure, Function and Genetics, vol. 37, no. SUPPL. 3, pp. 55-60. https://doi.org/10.1002/(SICI)1097-0134(1999)37:3+<55::AID-PROT8>3.0.CO;2-B

TY - JOUR

T1 - An iterative structure-assisted approach to sequence alignment and comparative modeling

AU - Burke, David F.

AU - Deane, Charlotte M.

AU - Nagarajaram, Hampapathalu A.

AU - Campillo, Nuria

AU - Martin-Martinez, Mercedes

AU - Mendes, Joaquim

AU - Molina, Franck

AU - Perry, Jeff

AU - Reddy, B. V.B.

AU - Soares, Claudio M.

AU - Steward, Robert E.

AU - Williams, Mark

AU - Carrondo, Maria Armenia

AU - Blundell, Tom L.

AU - Mizuguchi, Kenji

PY - 1999

Y1 - 1999

N2 - Correct alignment of the sequence of a target protein with those of homologues of known three-dimensional structure is a key step in comparative modeling. Usually an iterative approach that takes account of the local and overall structural features is required. We describe such an approach that exploits databases of structural alignments of homologous proteins (HOMSTRAD, http://www-cryst.bioc.cam.ac.uk/homstrad) and protein superfamilies (CAMPASS, http://www-cryst.bioc.cam.ac.uk/campass), in which structure-based alignments are analyzed and formatted with the program JOY (http://www- cryst.bioc.cam.ac.uk/joy) to reveal conserved local structural features. The databases facilitate the recognition of a family or superfamily, they assist in the selection of useful parent structures, they are helpful in alignment of the target sequences with the parent set, and are useful for deriving relationships that can be used in validating models. In the iterative approach, a model is constructed on the basis of the proposed sequence alignment and this is then reexpressed in the JOY format and realigned with the parent set. This is repeated until the model and sequence alignment is optimized. We examine the case for comparison and use of multiple structures of family members, rather than a single parent structure. We use the targets attempted by our group in CASP3 to assess the value of such procedures.

AB - Correct alignment of the sequence of a target protein with those of homologues of known three-dimensional structure is a key step in comparative modeling. Usually an iterative approach that takes account of the local and overall structural features is required. We describe such an approach that exploits databases of structural alignments of homologous proteins (HOMSTRAD, http://www-cryst.bioc.cam.ac.uk/homstrad) and protein superfamilies (CAMPASS, http://www-cryst.bioc.cam.ac.uk/campass), in which structure-based alignments are analyzed and formatted with the program JOY (http://www- cryst.bioc.cam.ac.uk/joy) to reveal conserved local structural features. The databases facilitate the recognition of a family or superfamily, they assist in the selection of useful parent structures, they are helpful in alignment of the target sequences with the parent set, and are useful for deriving relationships that can be used in validating models. In the iterative approach, a model is constructed on the basis of the proposed sequence alignment and this is then reexpressed in the JOY format and realigned with the parent set. This is repeated until the model and sequence alignment is optimized. We examine the case for comparison and use of multiple structures of family members, rather than a single parent structure. We use the targets attempted by our group in CASP3 to assess the value of such procedures.

KW - Alignment annotation

KW - Alignment databases

KW - Local structural features

KW - Loop modeling

KW - Model evaluation

KW - Protein family

KW - Protein structure

KW - Side-chain modeling

KW - Structure prediction

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U2 - 10.1002/(SICI)1097-0134(1999)37:3+<55::AID-PROT8>3.0.CO;2-B

DO - 10.1002/(SICI)1097-0134(1999)37:3+<55::AID-PROT8>3.0.CO;2-B

M3 - Article

C2 - 10526352

AN - SCOPUS:0032613202

SN - 0887-3585

VL - 37

SP - 55

EP - 60

JO - Proteins: Structure, Function and Genetics

JF - Proteins: Structure, Function and Genetics

IS - SUPPL. 3

ER -

An iterative structure-assisted approach to sequence alignment and comparative modeling

Abstract

Keywords

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