The computation of the global minimum energy conformation (GMEC) is an important and challenging topic in structure-based computational protein design. In this paper, we propose a new protein design algorithm based on the AND OR branch-and-bound (AOBB) search, which is a variant of the traditional branch-and-bound search algorithm, to solve this combinatorial optimization problem. By integrating with a powerful heuristic function, AOBB is able to fully exploit the graph structure of the underlying residue interaction network of a backbone template to significantly accelerate the design process. Tests on real protein data show that our new protein design algorithm is able to solve many prob- lems that were previously unsolvable by the traditional exact search algorithms, and for the problems that can be solved with traditional provable algorithms, our new method can provide a large speedup by several orders of magnitude while still guaranteeing to find the global minimum energy conformation (GMEC) solution.
The traditional BnB search algorithm @cite_0 usually ignores the underlying topological information of the residue interaction network constructed based on the backbone template, while AOBB is designed to exploit this property.
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Logarithmic search data structures, such as search trees and skiplists, are fundamental building blocks of many applications. Although the self-balancing binary search trees are among the most ubiquitous sequential search data structures, designing non-blocking rebalancing algorithms is challenging due to the required structural alternation, which may stall other concurrent operations. Skiplists, which probabilistically create multiple levels of shortcuts in an ordered list, provide practical alternatives to balanced search trees. The use of skiplists eliminates the need of rebalancing and ensures amortized logarithmic sequential search time, but concurrency is limited under write-dominated workload because the linkage between multiple distant nodes must be updated. In this paper, we present a linearizable lock-free dictionary design based on a multi-dimensional list (MDList). A node in an MDList arranges its child nodes by their dimensionality and order them by coordinate prefixes. The search operation works by first generating a one-to-one mapping from the scalar keys to a high-dimensional vectors space, then uniquely locating the target position by using the vector as coordinates. Our algorithm guarantees worst-case search time of O(log N) where N is the size of key space. Moreover, the ordering property of the data structure is readily maintained during mutations without rebalancing nor randomization. In our experimental evaluation using a micro-benchmark, our dictionary outperforms the state of the art approaches by as much as 100 when the key universe is large and an average of 30 across all scenarios.