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Methods for Molecular Modelling of Protein Complexes

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dc.contributor.author KANITKAR, TEJASHREE RAJARAM
dc.contributor.author SEN, NEELADRI
dc.contributor.author NAIR, SANJANA
dc.contributor.author SONI, NEELESH
dc.contributor.author AMRITKAR, KAUSTUBH
dc.contributor.author YAMTIRTHA, YOGENDRA
dc.contributor.author MADHUSUDHAN, M. S.
dc.contributor.editor Owens, Raymond J.
dc.date.accessioned 2022-04-03T14:17:22Z
dc.date.available 2022-04-03T14:17:22Z
dc.date.issued 2021-05
dc.identifier.citation Structural Proteomics, 53-80. en_US
dc.identifier.isbn 978-1-0716-1406-8
dc.identifier.isbn 978-1-0716-1405-1
dc.identifier.uri https://link.springer.com/protocol/10.1007/978-1-0716-1406-8_3 en_US
dc.identifier.uri http://dr.iiserpune.ac.in:8080/xmlui/handle/123456789/6693
dc.description.abstract Biological processes are often mediated by complexes formed between proteins and various biomolecules. The 3D structures of such protein–biomolecule complexes provide insights into the molecular mechanism of their action. The structure of these complexes can be predicted by various computational methods. Choosing an appropriate method for modelling depends on the category of biomolecule that a protein interacts with and the availability of structural information about the protein and its interacting partner. We intend for the contents of this chapter to serve as a guide as to what software would be the most appropriate for the type of data at hand and the kind of 3D complex structure required. Particularly, we have dealt with protein–small molecule ligand, protein–peptide, protein–protein, and protein–nucleic acid interactions. Most, if not all, model building protocols perform some sampling and scoring. Typically, several alternate conformations and configurations of the interactors are sampled. Each such sample is then scored for optimization. To boost the confidence in these predicted models, their assessment using other independent scoring schemes besides the inbuilt/default ones would prove to be helpful. This chapter also lists such software and serves as a guide to gauge the fidelity of modelled structures of biomolecular complexes. en_US
dc.language.iso en en_US
dc.publisher Springer Nature en_US
dc.subject Molecular docking en_US
dc.subject Protein-biomolecular complexes en_US
dc.subject 3D structure modelling en_US
dc.subject Scoring and sampling en_US
dc.subject 2021 en_US
dc.title Methods for Molecular Modelling of Protein Complexes en_US
dc.type Book chapter en_US
dc.contributor.department Dept. of Biology en_US
dc.title.book Structural Proteomics. en_US
dc.identifier.doi https://doi.org/10.1007/978-1-0716-1406-8_3 en_US
dc.identifier.sourcetitle Structural Proteomics en_US
dc.publication.originofpublisher Foreign en_US


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