Lamiable Alexis, Thévenet Pierre, Eustache Stephanie, Saladin Adrien, Moroy Gautier, Tuffery Pierre
Université Paris Diderot, Sorbonne Paris Cité, Molécules Thérapeutiques In Silico, Inserm UMR-S 973, 35 rue Hélène Brion, 75013, Paris, France.
Methods Mol Biol. 2017;1561:21-34. doi: 10.1007/978-1-4939-6798-8_3.
The blind identification of candidate patches of interaction on the protein surface is a difficult task that can hardly be accomplished without a heuristic or the use of simplified representations to speed up the search. The PEP-SiteFinder protocol performs a systematic blind search on the protein surface using a rigid docking procedure applied to a limited set of peptide suboptimal conformations expected to approximate satisfactorily the conformation of the peptide in interaction. All steps rely on a coarse-grained representation of the protein and the peptide. While simple, such a protocol can help to infer useful information, assuming a critical analysis of the results. Moreover, such a protocol can be extended to a semi-flexible protocol where the suboptimal conformations are directly folded in the vicinity of the receptor.
在蛋白质表面盲目识别相互作用的候选片段是一项艰巨的任务，若不采用启发式方法或使用简化表示来加速搜索，几乎无法完成。PEP-SiteFinder协议使用刚性对接程序对蛋白质表面进行系统的盲目搜索，该对接程序应用于一组有限的肽次优构象，这些构象预期能令人满意地近似相互作用中肽的构象。所有步骤都依赖于蛋白质和肽的粗粒度表示。虽然简单，但假设对结果进行批判性分析，这样的协议有助于推断有用信息。此外，这样的协议可以扩展为半灵活协议，其中次优构象直接在受体附近折叠。
