Overcoming sequence misalignments with weighted structural superposition.
Overcoming sequence misalignments with weighted structural superposition.
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DOI：
10.1002/prot.24134
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发表时间：
2012-11
影响因子：
2.9
通讯作者：
Carlson, Heather A.
中科院分区：
文献类型：
--
作者：
Khazanov, Nickolay A.;Damm-Ganamet, Kelly L.;Quang, Daniel X.;Carlson, Heather A.
An appropriate structural superposition identifies similarities and differences between homologous proteins that are not evident from sequence alignments alone. We have coupled our Gaussian-weighted RMSD (wRMSD) tool with a sequence aligner and seed extension (SE) algorithm to create a robust technique for overlaying structures and aligning sequences of homologous proteins (HwRMSD). HwRMSD overcomes errors in the initial sequence alignment that would normally propagate into a standard RMSD overlay. SE can generate a corrected sequence alignment from the improved structural superposition obtained by wRMSD. HwRMSD’s robust performance and its superiority over standard RMSD are demonstrated over a range of homologous proteins. Its better overlay results in corrected sequence alignments with good agreement to HOMSTRAD. Finally, HwRMSD is compared to established structural alignment methods: FATCAT, SSM, CE, and Dalilite. Most methods are comparable at placing residue pairs within 2 Å, but HwRMSD places many more residue pairs within 1 Å, providing a clear advantage. Such high accuracy is essential in drug design, where small distances can have a large impact on computational predictions. This level of accuracy is also needed to correct sequence alignments in an automated fashion, especially for omics-scale analysis. HwRMSD can align homologs with low sequence identity and large conformational differences, cases where both sequence-based and structural-based methods may fail. The HwRMSD pipeline overcomes the dependency of structural overlays on initial sequence pairing and removes the need to determine the best sequence-alignment method, substitution matrix, and gap parameters for each unique pair of homologs.
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影响因子：
16
作者：
Marino, M;Braun, L;Ghosh, P
通讯作者：
Ghosh, P
DOI：
10.1107/s0907444995016477
发表时间：
1996-07-01
期刊：
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
影响因子：
--
作者：
Kleywegt, GJ
通讯作者：
Kleywegt, GJ
影响因子：
64.5
作者：
Ditzel, L;Löwe, J;Steinbacher, S
通讯作者：
Steinbacher, S
DOI：
10.1107/s0907444904026460
发表时间：
2004-12-01
影响因子：
2.2
作者：
Krissinel, E;Henrick, K
通讯作者：
Henrick, K
结合MOAD，一种高质量的蛋白质配体数据库。
影响因子：
14.9
作者：
Benson, Mark L.;Smith, Richard D.;Khazanov, Nickolay A.;Dimcheff, Brandon;Beaver, John;Dresslar, Peter;Nerothin, Jason;Carlson, Heather A.
通讯作者：
Carlson, Heather A.