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Computational Analysis of Energy Landscapes Reveals Dynamic Features That Contribute to Binding of Inhibitors to CFTR-Associated Ligand.

Holt GT, Jou JD, Gill NP, Lowegard AU, Martin JW, Madden DR, Donald BR.

J Phys Chem B. 2019 Dec 12;123(49):10441-10455. doi: 10.1021/acs.jpcb.9b07278. Epub 2019 Nov 27.


Protein Design by Provable Algorithms.

Hallen MA, Donald BR.

Commun ACM. 2019 Oct;62(10):76-84. doi: 10.1145/3338124. No abstract available.


Toward Broad Spectrum Dihydrofolate Reductase Inhibitors Targeting Trimethoprim Resistant Enzymes Identified in Clinical Isolates of Methicillin Resistant Staphylococcus aureus.

Reeve SM, Si D, Krucinska J, Yan Y, Viswanathan K, Wang S, Holt GT, Frenkel MS, Ojewole AA, Estrada A, Agabiti SS, Alverson JB, Gibson ND, Priestley ND, Wiemer AJ, Donald BR, Wright DL.

ACS Infect Dis. 2019 Nov 8;5(11):1896-1906. doi: 10.1021/acsinfecdis.9b00222. Epub 2019 Oct 15.


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.

J Comput Chem. 2018 Nov 15;39(30):2494-2507. doi: 10.1002/jcc.25522. Epub 2018 Oct 14.


Continuous Interdomain Orientation Distributions Reveal Components of Binding Thermodynamics.

Qi Y, Martin JW, Barb AW, Thélot F, Yan AK, Donald BR, Oas TG.

J Mol Biol. 2018 Sep 14;430(18 Pt B):3412-3426. doi: 10.1016/j.jmb.2018.06.022. Epub 2018 Jun 18.


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.

Ojewole AA, Jou JD, Fowler VG, Donald BR.

J Comput Biol. 2018 Jul;25(7):726-739. doi: 10.1089/cmb.2017.0267. Epub 2018 Mar 13.


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

Hallen MA, Donald BR.

Bioinformatics. 2017 Jul 15;33(14):i5-i12. doi: 10.1093/bioinformatics/btx277.


A critical analysis of computational protein design with sparse residue interaction graphs.

Jain S, Jou JD, Georgiev IS, Donald BR.

PLoS Comput Biol. 2017 Mar 30;13(3):e1005346. doi: 10.1371/journal.pcbi.1005346. eCollection 2017 Mar.


OSPREY Predicts Resistance Mutations Using Positive and Negative Computational Protein Design.

Ojewole A, Lowegard A, Gainza P, Reeve SM, Georgiev I, Anderson AC, Donald BR.

Methods Mol Biol. 2017;1529:291-306.


Parallel Computational Protein Design.

Zhou Y, Donald BR, Zeng J.

Methods Mol Biol. 2017;1529:265-277.


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.

J Comput Biol. 2017 Jun;24(6):536-546. doi: 10.1089/cmb.2016.0136. Epub 2016 Sep 28.


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.

J Comput Biol. 2016 Sep;23(9):737-49. doi: 10.1089/cmb.2015.0234. Epub 2016 May 6.


Algorithms for protein design.

Gainza P, Nisonoff HM, Donald BR.

Curr Opin Struct Biol. 2016 Aug;39:16-26. doi: 10.1016/ Epub 2016 Apr 14. Review.


Fast search algorithms for computational protein design.

Traoré S, Roberts KE, Allouche D, Donald BR, André I, Schiex T, Barbe S.

J Comput Chem. 2016 May 5;37(12):1048-58. doi: 10.1002/jcc.24290. Epub 2016 Feb 2.


BWM*: A Novel, Provable, Ensemble-based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design.

Jou JD, Jain S, Georgiev IS, Donald BR.

J Comput Biol. 2016 Jun;23(6):413-24. doi: 10.1089/cmb.2015.0194. Epub 2016 Jan 8.


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

Roberts KE, Gainza P, Hallen MA, Donald BR.

Proteins. 2015 Oct;83(10):1859-1877. doi: 10.1002/prot.24870. Epub 2015 Aug 24.


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.

Nat Struct Mol Biol. 2015 Jul;22(7):522-31. doi: 10.1038/nsmb.3051. Epub 2015 Jun 22.


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

Hallen MA, Gainza P, Donald BR.

J Chem Theory Comput. 2015 May 12;11(5):2292-306.


Improved energy bound accuracy enhances the efficiency of continuous protein design.

Roberts KE, Donald BR.

Proteins. 2015 Jun;83(6):1151-64. doi: 10.1002/prot.24808. Epub 2015 May 8.


Systematic solution to homo-oligomeric structures determined by NMR.

Martin JW, Zhou P, Donald BR.

Proteins. 2015 Apr;83(4):651-61. doi: 10.1002/prot.24768. Epub 2015 Feb 5.


Protein design algorithms predict viable resistance to an experimental antifolate.

Reeve SM, Gainza P, Frey KM, Georgiev I, Donald BR, Anderson AC.

Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):749-54. doi: 10.1073/pnas.1411548112. Epub 2014 Dec 31.


Enhanced potency of a broadly neutralizing HIV-1 antibody in vitro improves protection against lentiviral infection in vivo.

Rudicell RS, Kwon YD, Ko SY, Pegu A, Louder MK, Georgiev IS, Wu X, Zhu J, Boyington JC, Chen X, Shi W, Yang ZY, Doria-Rose NA, McKee K, O'Dell S, Schmidt SD, Chuang GY, Druz A, Soto C, Yang Y, Zhang B, Zhou T, Todd JP, Lloyd KE, Eudailey J, Roberts KE, Donald BR, Bailer RT, Ledgerwood J; NISC Comparative Sequencing Program, Mullikin JC, Shapiro L, Koup RA, Graham BS, Nason MC, Connors M, Haynes BF, Rao SS, Roederer M, Kwong PD, Mascola JR, Nabel GJ.

J Virol. 2014 Nov;88(21):12669-82. doi: 10.1128/JVI.02213-14. Epub 2014 Aug 20.


An efficient parallel algorithm for accelerating computational protein design.

Zhou Y, Xu W, Donald BR, Zeng J.

Bioinformatics. 2014 Jun 15;30(12):i255-i263. doi: 10.1093/bioinformatics/btu264.


Auditory synapses to song premotor neurons are gated off during vocalization in zebra finches.

Hamaguchi K, Tschida KA, Yoon I, Donald BR, Mooney R.

Elife. 2014 Feb 18;3:e01833. doi: 10.7554/eLife.01833.


Structure of an HIV-1-neutralizing antibody target, the lipid-bound gp41 envelope membrane proximal region trimer.

Reardon PN, Sage H, Dennison SM, Martin JW, Donald BR, Alam SM, Haynes BF, Spicer LD.

Proc Natl Acad Sci U S A. 2014 Jan 28;111(4):1391-6. doi: 10.1073/pnas.1309842111. Epub 2014 Jan 13.


Intracellular Neural Recording with Pure Carbon Nanotube Probes.

Yoon I, Hamaguchi K, Borzenets IV, Finkelstein G, Mooney R, Donald BR.

PLoS One. 2013 Jun 19;8(6):e65715. doi: 10.1371/journal.pone.0065715. Print 2013.


Planning and Control for Microassembly of Structures Composed of Stress-Engineered MEMS Microrobots.

Donald BR, Levey CG, Paprotny I, Rus D.

Int J Rob Res. 2013 Feb 1;32(2):218-246.


OSPREY: protein design with ensembles, flexibility, and provable algorithms.

Gainza P, Roberts KE, Georgiev I, Lilien RH, Keedy DA, Chen CY, Reza F, Anderson AC, Richardson DC, Richardson JS, Donald BR.

Methods Enzymol. 2013;523:87-107. doi: 10.1016/B978-0-12-394292-0.00005-9.


HASH: a program to accurately predict protein Hα shifts from neighboring backbone shifts.

Zeng J, Zhou P, Donald BR.

J Biomol NMR. 2013 Jan;55(1):105-18. doi: 10.1007/s10858-012-9693-7. Epub 2012 Dec 16.


The role of local backrub motions in evolved and designed mutations.

Keedy DA, Georgiev I, Triplett EB, Donald BR, Richardson DC, Richardson JS.

PLoS Comput Biol. 2012;8(8):e1002629. doi: 10.1371/journal.pcbi.1002629. Epub 2012 Aug 2.


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

Hallen MA, Keedy DA, Donald BR.

Proteins. 2013 Jan;81(1):18-39. doi: 10.1002/prot.24150. Epub 2012 Sep 18.


Ultra-sharp metal and nanotube-based probes for applications in scanning microscopy and neural recording.

Borzenets IV, Yoon I, Prior MM, Donald BR, Mooney RD, Finkelstein G.

J Appl Phys. 2012 Apr 1;111(7):74703-747036. Epub 2012 Apr 12.


Computational design of a PDZ domain peptide inhibitor that rescues CFTR activity.

Roberts KE, Cushing PR, Boisguerin P, Madden DR, Donald BR.

PLoS Comput Biol. 2012;8(4):e1002477. doi: 10.1371/journal.pcbi.1002477. Epub 2012 Apr 19.


Protein design using continuous rotamers.

Gainza P, Roberts KE, Donald BR.

PLoS Comput Biol. 2012 Jan;8(1):e1002335. doi: 10.1371/journal.pcbi.1002335. Epub 2012 Jan 12.


Protein loop closure using orientational restraints from NMR data.

Tripathy C, Zeng J, Zhou P, Donald BR.

Proteins. 2012 Feb;80(2):433-53. doi: 10.1002/prot.23207. Epub 2011 Dec 13.


A geometric arrangement algorithm for structure determination of symmetric protein homo-oligomers from NOEs and RDCs.

Martin JW, Yan AK, Bailey-Kellogg C, Zhou P, Donald BR.

J Comput Biol. 2011 Nov;18(11):1507-23. doi: 10.1089/cmb.2011.0173. Epub 2011 Oct 28.


A Bayesian approach for determining protein side-chain rotamer conformations using unassigned NOE data.

Zeng J, Roberts KE, Zhou P, Donald BR.

J Comput Biol. 2011 Nov;18(11):1661-79. doi: 10.1089/cmb.2011.0172. Epub 2011 Oct 4.


NMR structural inference of symmetric homo-oligomers.

Chandola H, Yan AK, Potluri S, Donald BR, Bailey-Kellogg C.

J Comput Biol. 2011 Dec;18(12):1757-75. doi: 10.1089/cmb.2010.0327. Epub 2011 Jun 30.


Protein side-chain resonance assignment and NOE assignment using RDC-defined backbones without TOCSY data.

Zeng J, Zhou P, Donald BR.

J Biomol NMR. 2011 Aug;50(4):371-95. doi: 10.1007/s10858-011-9522-4. Epub 2011 Jun 25.


NVR-BIP: Nuclear Vector Replacement using Binary Integer Programming for NMR Structure-Based Assignments.

Apaydin MS, Çatay B, Patrick N, Donald BR.

Comput J. 2011 May 1;54(5):708-716.


A graphical method for analyzing distance restraints using residual dipolar couplings for structure determination of symmetric protein homo-oligomers.

Martin JW, Yan AK, Bailey-Kellogg C, Zhou P, Donald BR.

Protein Sci. 2011 Jun;20(6):970-85. doi: 10.1002/pro.620. Epub 2011 Apr 27.


Predicting resistance mutations using protein design algorithms.

Frey KM, Georgiev I, Donald BR, Anderson AC.

Proc Natl Acad Sci U S A. 2010 Aug 3;107(31):13707-12. doi: 10.1073/pnas.1002162107. Epub 2010 Jul 19.


Automated NMR Assignment and Protein Structure Determination using Sparse Dipolar Coupling Constraints.

Donald BR, Martin J.

Prog Nucl Magn Reson Spectrosc. 2009 Aug 1;55(2):101-127. No abstract available.


High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations.

Zeng J, Boyles J, Tripathy C, Wang L, Yan A, Zhou P, Donald BR.

J Biomol NMR. 2009 Nov;45(3):265-81. doi: 10.1007/s10858-009-9366-3. Epub 2009 Aug 27.


Computational structure-based redesign of enzyme activity.

Chen CY, Georgiev I, Anderson AC, Donald BR.

Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3764-9. doi: 10.1073/pnas.0900266106. Epub 2009 Feb 19. Erratum in: Proc Natl Acad Sci U S A. 2009 May 5;106(18):7678.


Algorithm for backrub motions in protein design.

Georgiev I, Keedy D, Richardson JS, Richardson DC, Donald BR.

Bioinformatics. 2008 Jul 1;24(13):i196-204. doi: 10.1093/bioinformatics/btn169.


Structure-based protein NMR assignments using native structural ensembles.

Apaydin MS, Conitzer V, Donald BR.

J Biomol NMR. 2008 Apr;40(4):263-76. doi: 10.1007/s10858-008-9230-x. Epub 2008 Mar 26.


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