Hallen MA - Search Results

1

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.

Hallen MA, Donald BR. Hallen MA, et al. J Comput Biol. 2016 May;23(5):311-21. doi: 10.1089/cmb.2015.0188. Epub 2016 Jan 13. J Comput Biol. 2016. PMID: 26761641 Free PMC article.

2

cOSPREY: A Cloud-Based Distributed Algorithm for Large-Scale Computational Protein Design.

Pan Y, Dong Y, Zhou J, Hallen M, Donald BR, Zeng J, Xu W. Pan Y, et al. J Comput Biol. 2016 Sep;23(9):737-49. doi: 10.1089/cmb.2015.0234. Epub 2016 May 6. J Comput Biol. 2016. PMID: 27154509 Free PMC article.

3

Dead-end elimination with perturbations (DEEPer): a provable protein design algorithm with continuous sidechain and backbone flexibility.

Hallen MA, Keedy DA, Donald BR. Hallen MA, et al. Proteins. 2013 Jan;81(1):18-39. doi: 10.1002/prot.24150. Epub 2012 Sep 18. Proteins. 2013. PMID: 22821798 Free PMC article.

4

Fast gap-free enumeration of conformations and sequences for protein design.

Roberts KE, Gainza P, Hallen MA, Donald BR. Roberts KE, et al. Among authors: hallen ma. Proteins. 2015 Oct;83(10):1859-1877. doi: 10.1002/prot.24870. Epub 2015 Aug 24. Proteins. 2015. PMID: 26235965 Free PMC article.

5

LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid Rotamer-Like Efficiency.

Hallen MA, Jou JD, Donald BR. Hallen MA, et al. J Comput Biol. 2017 Jun;24(6):536-546. doi: 10.1089/cmb.2016.0136. Epub 2016 Sep 28. J Comput Biol. 2017. PMID: 27681371 Free PMC article.

6

CATS (Coordinates of Atoms by Taylor Series): protein design with backbone flexibility in all locally feasible directions.

Hallen MA, Donald BR. Hallen MA, et al. Bioinformatics. 2017 Jul 15;33(14):i5-i12. doi: 10.1093/bioinformatics/btx277. Bioinformatics. 2017. PMID: 28882005 Free PMC article.

7

OSPREY 3.0: Open-source protein redesign for you, with powerful new features.

Hallen MA, Martin JW, Ojewole A, Jou JD, Lowegard AU, Frenkel MS, Gainza P, Nisonoff HM, Mukund A, Wang S, Holt GT, Zhou D, Dowd E, Donald BR. Hallen MA, et al. J Comput Chem. 2018 Nov 15;39(30):2494-2507. doi: 10.1002/jcc.25522. Epub 2018 Oct 14. J Comput Chem. 2018. PMID: 30368845 Free PMC article.

8

Compact Representation of Continuous Energy Surfaces for More Efficient Protein Design.

Hallen MA, Gainza P, Donald BR. Hallen MA, et al. J Chem Theory Comput. 2015 May 12;11(5):2292-306. doi: 10.1021/ct501031m. J Chem Theory Comput. 2015. PMID: 26089744 Free PMC article.

9

Crystal structure, conformational fixation and entry-related interactions of mature ligand-free HIV-1 Env.

Kwon YD, Pancera M, Acharya P, Georgiev IS, Crooks ET, Gorman J, Joyce MG, Guttman M, Ma X, Narpala S, Soto C, Terry DS, Yang Y, Zhou T, Ahlsen G, Bailer RT, Chambers M, Chuang GY, Doria-Rose NA, Druz A, Hallen MA, Harned A, Kirys T, Louder MK, O'Dell S, Ofek G, Osawa K, Prabhakaran M, Sastry M, Stewart-Jones GB, Stuckey J, Thomas PV, Tittley T, Williams C, Zhang B, Zhao H, Zhou Z, Donald BR, Lee LK, Zolla-Pazner S, Baxa U, Schön A, Freire E, Shapiro L, Lee KK, Arthos J, Munro JB, Blanchard SC, Mothes W, Binley JM, McDermott AB, Mascola JR, Kwong PD. Kwon YD, et al. Among authors: hallen ma. Nat Struct Mol Biol. 2015 Jul;22(7):522-31. doi: 10.1038/nsmb.3051. Epub 2015 Jun 22. Nat Struct Mol Biol. 2015. PMID: 26098315 Free PMC article.

10

Protein Design by Provable Algorithms.

Hallen MA, Donald BR. Hallen MA, et al. Commun ACM. 2019 Oct;62(10):76-84. doi: 10.1145/3338124. Commun ACM. 2019. PMID: 31607753 Free PMC article.

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