ArticleJournal of computational biology : a journal of computational molecular cell biology2017
LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid Rotamer-Like Efficiency.
Article in Journal of computational biology : a journal of computational molecular cell biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Perturbing the energy landscape for improved packing during computational protein design.Proteins · 2021Article
- Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD:KRas protein-protein interface.PLoS computational biology · 2020Article
- Dynamics, a Powerful Component of Current and Future in Silico Approaches for Protein Design and Engineering.International journal of molecular sciences · 2020Review
- Minimization-Aware RecursiveJournal of computational biology : a journal of computational molecular cell biology · 2020Article
- Protein Design by Provable Algorithms.Communications of the ACM · 2019Article
- BBK* (Branch and Bound Over K*): A Provable and Efficient Ensemble-Based Protein Design Algorithm to Optimize Stability and Binding Affinity Over Large Sequence Spaces.Journal of computational biology : a journal of computational molecular cell biology · 2018Article
- CATS (Coordinates of Atoms by Taylor Series): protein design with backbone flexibility in all locally feasible directions.Bioinformatics (Oxford, England) · 2017Article
- A critical analysis of computational protein design with sparse residue interaction graphs.PLoS computational biology · 2017Article
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3 authors.
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Abstract
Most protein design algorithms search over discrete conformations and an energy function that is residue-pairwise, that is, a sum of terms that depend on the sequence and conformation of at most two residues. Although modeling of continuous flexibility and of non-residue-pairwise energies significantly increases the accuracy of protein design, previous methods to model these phenomena add a significant asymptotic cost to design calculations. We now remove this cost by modeling continuous flexibility and non-residue-pairwise energies in a form suitable for direct input to highly efficient, discrete combinatorial optimization algorithms such as DEE/A* or branch-width minimization. Our novel algorithm performs a local unpruned tuple expansion (LUTE), which can efficiently represent both continuous flexibility and general, possibly nonpairwise energy functions to an arbitrary level of accuracy using a discrete energy matrix. We show using 47 design calculation test cases that LUTE provides a dramatic speedup in both single-state and multistate continuously flexible designs.
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