NDLI: Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20

Content Provider	PubMed Central
Author	Kilambi, Krishna Praneeth Pacella, Michael S. Xu, Jianqing Labonte, Jason W. Porter, Justin R. Muthu, Pravin Drew, Kevin Kuroda, Daisuke Ora, Schueler-furman Bonneau, Richard Gray, Jeffrey J.
Copyright Year	2013
Abstract	Rounds 20–27 of the Critical Assessment of PRotein Interactions (CAPRI) provided a testing platform for computational methods designed to address a wide range of challenges. The diverse targets drove the creation of and new combinations of computational tools. In this study, RosettaDock and other novel Rosetta protocols were used to successfully predict four of the 10 blind targets. For example, for DNase domain of Colicin E2–Im2 immunity protein, RosettaDock and RosettaLigand were used to predict the positions of water molecules at the interface, recovering 46% of the native water-mediated contacts. For α-repeat Rep4–Rep2 and g-type lysozyme–PliG inhibitor complexes, homology models were built and standard and pH-sensitive docking algorithms were used to generate structures with interface RMSD values of 3.3 Å and 2.0 Å, respectively. A novel flexible sugar–protein docking protocol was also developed and used for structure prediction of the BT4661–heparin-like saccharide complex, recovering 71% of the native contacts. Challenges remain in the generation of accurate homology models for protein mutants and sampling during global docking. On proteins designed to bind influenza hemagglutinin, only about half of the mutations were identified that affect binding (T55: 54%; T56: 48%). The prediction of the structure of the xylanase complex involving homology modeling and multidomain docking pushed the limits of global conformational sampling and did not result in any successful prediction. The diversity of problems at hand requires computational algorithms to be versatile; the recent additions to the Rosetta suite expand the capabilities to encompass more biologically realistic docking problems.
Related Links	http://dx.doi.org/10.1002/prot.24425
Ending Page	2209
Page Count	9
Starting Page	2201
File Format	PDF
ISSN	08873585
e-ISSN	10970134
Journal	Proteins
Issue Number	12
Volume Number	81
Language	English
Publisher Date	2013-12-01
Access Restriction	Open
Subject Keyword	Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Structural Biology Biochemistry Molecular Biology

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A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13–19

Performance of ZDOCK in CAPRI rounds 20–26

A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19.

Blind Prediction of Interfacial Water Positions in CAPRI

Performance of ZDOCK and ZRANK in CAPRI Rounds 13 -19

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Selection of Near-Native Poses in CAPRI Rounds 13-19

MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15–19

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Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20–27

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