ArticleJournal of computational chemistry2016
Fast search algorithms for computational protein design.
Article in Journal of computational chemistry, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- A Generative Neuro-Symbolic AI for Protein Sequence Design.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Complete combinatorial mutational enumeration of a protein functional site enables sequence-landscape mapping and identifies highly-mutated variants that retain activity.Protein science : a publication of the Protein Society · 2024Article
- Identification, Characterization, and Computer-Aided Rational Design of a Novel Thermophilic Esterase from Geobacillus subterraneus, and Application in the Synthesis of Cinnamyl Acetate.Applied biochemistry and biotechnology · 2024Article
- 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
- Advances in protein structure prediction and design.Nature reviews. Molecular cell biology · 2019Review
- Protein Design by Provable Algorithms.Communications of the ACM · 2019Article
- Recent advances in automated protein design and its future challenges.Expert opinion on drug discovery · 2018Review
- 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
- LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid Rotamer-Like Efficiency.Journal of computational biology : a journal of computational molecular cell biology · 2017Article
- Algorithms for protein design.Current opinion in structural biology · 2016Review
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Authors and funding
7 authors.
Funding
Abstract
One of the main challenges in computational protein design (CPD) is the huge size of the protein sequence and conformational space that has to be computationally explored. Recently, we showed that state-of-the-art combinatorial optimization technologies based on Cost Function Network (CFN) processing allow speeding up provable rigid backbone protein design methods by several orders of magnitudes. Building up on this, we improved and injected CFN technology into the well-established CPD package Osprey to allow all Osprey CPD algorithms to benefit from associated speedups. Because Osprey fundamentally relies on the ability of A* to produce conformations in increasing order of energy, we defined new A* strategies combining CFN lower bounds, with new side-chain positioning-based branching scheme. Beyond the speedups obtained in the new A*-CFN combination, this novel branching scheme enables a much faster enumeration of suboptimal sequences, far beyond what is reachable without it. Together with the immediate and important speedups provided by CFN technology, these developments directly benefit to all the algorithms that previously relied on the DEE/ A* combination inside Osprey* and make it possible to solve larger CPD problems with provable algorithms.
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