comets (Constrained Optimization of Multistate Energies by Tree Search): A Provable and Efficient Protein Design Algorithm to Optimize Binding Affinity and Specificity with Respect to Sequence
نویسندگان
چکیده
Practical protein design problems require designing sequences with a combination of affinity, stability, and specificity requirements. Multistate protein design algorithms model multiple structural or binding "states" of a protein to address these requirements. comets provides a new level of versatile, efficient, and provable multistate design. It provably returns the minimum with respect to sequence of any desired linear combination of the energies of multiple protein states, subject to constraints on other linear combinations. Thus, it can target nearly any combination of affinity (to one or multiple ligands), specificity, and stability (for multiple states if needed). Empirical calculations on 52 protein design problems showed comets is far more efficient than the previous state of the art for provable multistate design (exhaustive search over sequences). comets can handle a very wide range of protein flexibility and can enumerate a gap-free list of the best constraint-satisfying sequences in order of objective function value.
منابع مشابه
Comets (Constrained Optimization of Multistate Energies by Tree Search): A Provable and Efficient Algorithm to Optimize Binding Affinity and Specificity with Respect to Sequence
Practical protein design problems require designing sequences with a combination of affinity, stability, and specificity requirements.Multistate protein design algorithms model multiple structural or binding “states” of a protein to address these requirements. comets provides a new level of versatile, efficient, and provable multistate design. It provably returns the minimum with respect to seq...
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(Constrained Optimization of Multi-state Energies by Tree Search): A provable and efficient protein design algorithm to optimize binding affinity and specificity with respect to sequence. Section A provides a highly simplified, " toy " example of a multistate protein design calculation to demonstrate the operation of comets. Section B provides details of the methods used to compute lower bounds...
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ورودعنوان ژورنال:
- Journal of computational biology : a journal of computational molecular cell biology
دوره 23 5 شماره
صفحات -
تاریخ انتشار 2016