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                  Rina Dechter},
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@article{AlLazikani2001-description-and-limitations-of-protein-structure-prediction,
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author = {Bissan Al-Lazikani and Joon Jung and Zhexin Xiang and Barry Honig},
keywords = {Protein structure prediction, CASP, PSI-BLAST, homology, alignment, loop prediction, side-chain prediction, SCOP},
}

@InProceedings{pezeshki2022uai-aobb-for-cpd-2022,
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  author =       {Pezeshki, Bobak and Marinescu, Radu and Ihler, Alexander and Dechter, Rina},
  booktitle = 	 {Proceedings of the Thirty-Eighth Conference on Uncertainty in Artificial Intelligence},
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  publisher =    {PMLR},
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}

@inproceedings{lam2014beyond,
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}

@Article{ruffini-diversity-and-optimality-cpd-cfns,
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    TITLE = {Guaranteed Diversity and Optimality in Cost Function Network Based Computational Protein Design Methods},
    JOURNAL = {Algorithms},
    VOLUME = {14},
    YEAR = {2021},
    NUMBER = {6},
    ARTICLE-NUMBER = {168},
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    _issn = {1999-4893},
}

@article{gainza2016algorithms,
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}

@article{jumper2021alphafold,
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  journal={Nature},
  volume={596},
  number={7873},
  pages={583--589},
  year={2021},
  publisher={Nature Publishing Group}
}

@article{huang2016coming,
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@inproceedings{kask20-scaling-up-as,
  title     = {Scaling Up AND/OR Abstraction Sampling},
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  booktitle = {Proceedings of the Twenty-Ninth International Joint Conference on
               Artificial Intelligence, {IJCAI-20}},
  publisher = {International Joint Conferences on Artificial Intelligence Organization},
  editor    = {Christian Bessiere},
  pages     = {4266--4274},
  year      = {2020},
  month     = {7},
  note      = {Main track},
  doi       = {10.24963/ijcai.2020/589},
  url       = {https://doi.org/10.24963/ijcai.2020/589},
}

@inproceedings{razeghi21-dbe,
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  booktitle = {Proceedings of the Thirtieth International Joint Conference on
               Artificial Intelligence, {IJCAI-21}},
  publisher = {International Joint Conferences on Artificial Intelligence Organization},
  editor    = {Zhi-Hua Zhou},
  pages     = {4235--4242},
  year      = {2021},
  month     = {8},
  note      = {Main Track},
  doi       = {10.24963/ijcai.2021/582},
  url       = {https://doi.org/10.24963/ijcai.2021/582},
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@article{vucinic19-positive-multistate-design,
author = {Vucinic, Jelena and Simoncini, David and Ruffini, Manon and Barbe, Sophie and Schiex, Thomas},
year = {2019},
month = {06},
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volume = {36},
journal = {Bioinformatics (Oxford, England)},
_doi = {10.1093/bioinformatics/btz497}
}

@article{viricel18-cfn-cpd,
author = {Viricel, Clement and de Givry, Simon and Schiex, Thomas and Barbe, Sophie},
year = {2018},
month = {02},
pages = {},
title = {Cost Function Network-based Design of Protein-Protein Interactions: predicting changes in binding affinity},
volume = {34},
journal = {Bioinformatics (Oxford, England)},
_doi = {10.1093/bioinformatics/bty092}
}

@inproceedings{lilien04-protein-redesign,
author = {Lilien, Ryan H. and Stevens, Brian W. and Anderson, Amy C. and Donald, Bruce R.},
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_doi = {10.1145/974614.974622},
booktitle = {Proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology},
pages = {46–57},
numpages = {12},
keywords = {protein design, fluorescence binding assay, protein-ligand binding, non-ribosomal peptide synthetase, protein flexibility, molecular ensemble, enzyme design},
location = {San Diego, California, USA},
series = {RECOMB '04}
}

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@article{hallen18-osprey-3,
author = {Hallen, Mark and Martin, Jeffrey and Ojewole, Adegoke and Jou, Jonathan and Lowegard, Anna and Frenkel, Marcel and Gainza, Pablo and Nisonoff, Hunter and Mukund, Aditya and Wang, Siyu and Holt, Graham and Zhou, David and Dowd, Elizabeth and Donald, Bruce},
year = {2018},
month = {10},
pages = {},
title = {OSPREY 3.0: Open-source protein redesign for you, with powerful new features},
volume = {39},
journal = {Journal of Computational Chemistry},
_doi = {10.1002/jcc.25522}
}

@Article{defresne-protein-design-with-deep-learning,
AUTHOR = {Defresne, Marianne and Barbe, Sophie and Schiex, Thomas},
TITLE = {Protein Design with Deep Learning},
JOURNAL = {International Journal of Molecular Sciences},
VOLUME = {22},
YEAR = {2021},
NUMBER = {21},
ARTICLE-NUMBER = {11741},
_URL = {https://www.mdpi.com/1422-0067/22/21/11741},
_PubMedID = {34769173},
_ISSN = {1422-0067},
ABSTRACT = {Computational Protein Design (CPD) has produced impressive results for engineering new proteins, resulting in a wide variety of applications. In the past few years, various efforts have aimed at replacing or improving existing design methods using Deep Learning technology to leverage the amount of publicly available protein data. Deep Learning (DL) is a very powerful tool to extract patterns from raw data, provided that data are formatted as mathematical objects and the architecture processing them is well suited to the targeted problem. In the case of protein data, specific representations are needed for both the amino acid sequence and the protein structure in order to capture respectively 1D and 3D information. As no consensus has been reached about the most suitable representations, this review describes the representations used so far, discusses their strengths and weaknesses, and details their associated DL architecture for design and related tasks.},
_DOI = {10.3390/ijms222111741}
}

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               Jonathan D. Jou and
               Vance G. Fowler and
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               Ensemble-Based Protein Design Algorithm to Optimize Stability and
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@article{marinescu18-jair-AO-search-mmap,
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@article{dechter-book-2ndEd,
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@inproceedings{marinescu18-stochastic-anytime-mmap,
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@article{hallenProvableAlgsCPD,
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_doi = {10.1145/3338124},
abstract = {Protein design algorithms can leverage provable guarantees of accuracy to provide new insights and unique optimized molecules.},
journal = {Commun. ACM},
month = {sep},
pages = {76–84},
numpages = {9}
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  pages     = {632--641},
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@inproceedings{DBLP:conf/aaai/LouDI17,
  author    = {Qi Lou and
               Rina Dechter and
               Alexander. Ihler},
  title     = {Anytime Anyspace {AND/OR} Search for Bounding the Partition Function},
  booktitle = {Proceedings of the Thirty-First {AAAI} Conference on Artificial Intelligence,
               February 4-9, 2017, San Francisco, California, {USA.}},
  pages     = {860--867},
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@article{DBLP:journals/ai/LelisZH13,
	author    = {Levi H. S. Lelis and
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	Robert C. Holte},
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@article{LELIS201353,
	title = "Predicting the size of {IDA}*'s search tree",
	journal = "Artificial Intelligence",
	volume = "196",
	number = "Supplement C",
	pages = "53 - 76",
	year = "2013",
	_issn = "0004-3702",
	_doi = "https://doi.org/10.1016/j.artint.2013.01.001",
	_url = "http://www.sciencedirect.com/science/article/pii/S0004370213000039",
	author = "Levi H. S. Lelis and Sandra Zilles and Robert C. Holte",
	keywords = "Heuristic search, Predicting search performance"
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@inproceedings{DBLP:conf/cp/LelisOD14,
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	booktitle = {Principles and Practice of Constraint Programming - 20th International
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	pages     = {481--496},
	year      = {2014},
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@proceedings{DBLP:conf/cp/2014,
	editor    = {Barry O'Sullivan},
	title     = {Principles and Practice of Constraint Programming - 20th International
	Conference, {CP} 2014, Lyon, France, September 8-12, 2014. Proceedings},
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	volume    = {8656},
	publisher = {Springer},
	year      = {2014},
	url       = {http://dx.doi.org/10.1007/978-3-319-10428-7},
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	isbn      = {978-3-319-10427-0},
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@book{DBLP:series/synthesis/2013Dechter,
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  series    = {Synthesis Lectures on Artificial Intelligence and Machine Learning},
  publisher = {Morgan {\&} Claypool Publishers},
  year      = {2013},
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@article{Marinescu19-any-recursive-bf-search-for-bounding-mmap, 
title={Anytime Recursive Best-First Search for Bounding Marginal MAP}, volume={33}, _url={https://ojs.aaai.org/index.php/AAAI/article/view/4792}, _DOI={10.1609/aaai.v33i01.33017924}, 
number={01}, 
journal={Proceedings of the AAAI Conference on Artificial Intelligence}, 
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[R107] Abstract | PDF David Larkin. "Semi-Independent
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  title     = {Active Tuples-based Scheme for Bounding Posterior Beliefs},
  journal   = {J. Artif. Intell. Res. (JAIR)},
  volume    = {39},
  year      = {2010},
  pages     = {335-371},
  ee        = {http://dx.doi.org/10.1613/jair.2945},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}


@inproceedings{DBLP:conf/aaai/RollonD10,
  author    = {Emma Rollon and
               Rina Dechter},
  title     = {New Mini-Bucket Partitioning Heuristics for Bounding the
               Probability of Evidence},
  booktitle = {AAAI},
  year      = {2010},
  ee        = {http://www.aaai.org/ocs/index.php/AAAI/AAAI10/paper/view/1891},
  crossref  = {DBLP:conf/aaai/2010},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}


@inproceedings{DBLP:conf/nips/WexlerM08,
  author    = {Ydo Wexler and
               Christopher Meek},
  title     = {MAS: a multiplicative approximation scheme for probabilistic
               inference},
  booktitle = {NIPS},
  year      = {2008},
  pages     = {1761-1768},
  ee        = {http://books.nips.cc/papers/files/nips21/NIPS2008_0707.pdf},
  crossref  = {DBLP:conf/nips/2008},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}



@INPROCEEDINGS{Gomes97b,
    AUTHOR  = "Carla Gomes and Bart Selman and Nuno Crato",
    TITLE   = "{Heavy-Tailed Distributions in Combinatorial Search}",
    BOOKTITLE = "{Principles and Practice of Constraint
            Programming -- CP97}",
    EDITOR  = "Gert Smolka",
    YEAR    = "1997",
    PAGES   = "121-135"}

@INCOLLECTION{Jaumard96,
    AUTHOR  = "Brigette Jaumard and Mihnea Stan and Jacques Desrosiers",
    TITLE   = "{Tabu Search and a Quadratic Relaxation for the
            Satisfiability Problems}",
    BOOKTITLE = "{Cliques, Coloring, and Satifiability}",
    PUBLISHER = "American Mathematical Society",
    YEAR    = "1996",
    EDITOR  = "David S. Johnson and Michael A. Trick",
    SERIES  = "DIMACS Series in Discrete Mathematics and Theoretical
            Computer Science",
    VOLUME  = "26"}

@INPROCEEDINGS{Rish97,
    AUTHOR  = "Irina Rish and Daniel Frost",
    TITLE   = "Statistical Analysis of Backtracking on Inconsistent CSPs",
    BOOKTITLE = "{Principles and Practice of Constraint
            Programming -- CP97}",
    EDITOR  = "Gert Smolka",
    YEAR    = "1997",
    PAGES   = "150--162r"}

    @book{DBLP:books/fm/GareyJ79,
  author    = {M. R. Garey and
               David S. Johnson},
  title     = {Computers and Intractability: A Guide to the Theory of NP-Completeness},
  publisher = {W. H. Freeman},
  year      = {1979},
  isbn      = {0-7167-1044-7},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}
