| Year |
Citation |
Score |
| 2022 |
Wang S, Reeve SM, Holt GT, Ojewole AA, Frenkel MS, Gainza P, Keshipeddy S, Fowler VG, Wright DL, Donald BR. Chiral evasion and stereospecific antifolate resistance in Staphylococcus aureus. Plos Computational Biology. 18: e1009855. PMID 35143481 DOI: 10.1371/journal.pcbi.1009855 |
0.739 |
|
| 2020 |
Lowegard AU, Frenkel MS, Holt GT, Jou JD, Ojewole AA, Donald BR. 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. 16: e1007447. PMID 32511232 DOI: 10.1371/Journal.Pcbi.1007447 |
0.457 |
|
| 2019 |
Jou JD, Holt GT, Lowegard AU, Donald BR. Minimization-Aware Recursive A Novel, Provable Algorithm that Accelerates Ensemble-Based Protein Design and Provably Approximates the Energy Landscape. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 31855059 DOI: 10.1089/Cmb.2019.0315 |
0.493 |
|
| 2019 |
Holt GT, Jou JD, Gill NP, Lowegard AU, Martin JW, Madden DR, Donald BR. Computational Analysis of Energy Landscapes Reveals Dynamic Features that Contribute to Binding of Inhibitors to CFTR-Associated Ligand. The Journal of Physical Chemistry. B. PMID 31697075 DOI: 10.1021/Acs.Jpcb.9B07278 |
0.375 |
|
| 2019 |
Hallen MA, Donald BR. Protein Design by Provable Algorithms. Communications of the Acm. 62: 76-84. PMID 31607753 DOI: 10.1145/3338124 |
0.453 |
|
| 2019 |
Reeve SM, Si D, Krucinska J, Yan Y, Viswanathan K, Wang S, Holt GT, Frenkel MS, Ojewole A, Estrada A, Agabiti SS, Alverson JB, Gibson ND, Priestly ND, Wiemer AJ, ... Donald BR, et al. Toward Broad Spectrum DHFR inhibitors Targeting Trimethoprim Resistant Enzymes Identified in Clinical Isolates of Methicillin-Resistant Staphylococcus aureus. Acs Infectious Diseases. PMID 31565920 DOI: 10.1021/Acsinfecdis.9B00222 |
0.728 |
|
| 2019 |
Lavor C, Liberti L, Donald B, Worley B, Bardiaux B, Malliavin TE, Nilges M. Minimal NMR distance information for rigidity of protein graphs. Discrete Applied Mathematics (Amsterdam, Netherlands : 1988). 256: 91-104. PMID 30799888 DOI: 10.1016/J.Dam.2018.03.071 |
0.44 |
|
| 2018 |
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. OSPREY 3.0: Open-source protein redesign for you, with powerful new features. Journal of Computational Chemistry. PMID 30368845 DOI: 10.1002/Jcc.25522 |
0.441 |
|
| 2018 |
Qi Y, Martin JW, Barb AW, Thélot F, Yan A, Donald BR, Oas TG. Continuous Interdomain Orientation Distributions Reveal Components of Binding Thermodynamics. Journal of Molecular Biology. PMID 29924964 DOI: 10.1016/J.Jmb.2018.06.022 |
0.771 |
|
| 2018 |
Ojewole AA, Jou JD, Fowler VG, Donald BR. 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. PMID 29641249 DOI: 10.1089/Cmb.2017.0267 |
0.451 |
|
| 2018 |
Lowegard A, Frenkel M, Donald B. Predicting the Effect of Mutations in the KRas/c-Raf-RBD Protein-Protein Interface Biophysical Journal. 114. DOI: 10.1016/J.Bpj.2017.11.3151 |
0.338 |
|
| 2017 |
Hallen MA, Donald BR. CATS (Coordinates of Atoms by Taylor Series): protein design with backbone flexibility in all locally feasible directions. Bioinformatics (Oxford, England). 33: i5-i12. PMID 28882005 DOI: 10.1093/Bioinformatics/Btx277 |
0.48 |
|
| 2017 |
Jain S, Jou JD, Georgiev IS, Donald BR. A critical analysis of computational protein design with sparse residue interaction graphs. Plos Computational Biology. 13: e1005346. PMID 28358804 DOI: 10.1371/Journal.Pcbi.1005346 |
0.68 |
|
| 2017 |
Ojewole A, Lowegard A, Gainza P, Reeve SM, Georgiev I, Anderson AC, Donald BR. OSPREY Predicts Resistance Mutations Using Positive and Negative Computational Protein Design. Methods in Molecular Biology (Clifton, N.J.). 1529: 291-306. PMID 27914058 DOI: 10.1007/978-1-4939-6637-0_15 |
0.798 |
|
| 2017 |
Zhou Y, Donald BR, Zeng J. Parallel Computational Protein Design. Methods in Molecular Biology (Clifton, N.J.). 1529: 265-277. PMID 27914056 DOI: 10.1007/978-1-4939-6637-0_13 |
0.728 |
|
| 2016 |
Hallen MA, Jou JD, Donald BR. 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. PMID 27681371 DOI: 10.1089/cmb.2016.0136 |
0.324 |
|
| 2016 |
Pan Y, Dong Y, Zhou J, Hallen M, Donald BR, Zeng J, Xu W. cOSPREY: A Cloud-Based Distributed Algorithm for Large-Scale Computational Protein Design. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 27154509 DOI: 10.1089/Cmb.2015.0234 |
0.701 |
|
| 2016 |
Gainza P, Nisonoff HM, Donald BR. Algorithms for protein design. Current Opinion in Structural Biology. 39: 16-26. PMID 27086078 DOI: 10.1016/J.Sbi.2016.03.006 |
0.488 |
|
| 2016 |
Traoré S, Roberts KE, Allouche D, Donald BR, André I, Schiex T, Barbe S. Fast search algorithms for computational protein design. Journal of Computational Chemistry. PMID 26833706 DOI: 10.1002/Jcc.24290 |
0.471 |
|
| 2016 |
Hallen MA, Donald BR. 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. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 26761641 DOI: 10.1089/Cmb.2015.0188 |
0.437 |
|
| 2016 |
Jou JD, Jain S, Georgiev IS, Donald BR. BWM*: A Novel, Provable, Ensemble-based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 26744898 DOI: 10.1089/Cmb.2015.0194 |
0.7 |
|
| 2016 |
Hallen MA, Jou JD, Donald BR. LUTE (Local unpruned tuple expansion): Accurate continuously flexible protein design with general energy functions and rigid-rotamer-like efficiency Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9649: 122-136. DOI: 10.1016/J.Bpj.2016.11.1077 |
0.433 |
|
| 2015 |
Roberts KE, Gainza P, Hallen MA, Donald BR. Fast gap-free enumeration of conformations and sequences for protein design. Proteins. 83: 1859-77. PMID 26235965 DOI: 10.1002/Prot.24870 |
0.523 |
|
| 2015 |
Do Kwon Y, 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, ... ... Donald BR, et al. Crystal structure, conformational fixation and entry-related interactions of mature ligand-free HIV-1 Env. Nature Structural & Molecular Biology. 22: 522-31. PMID 26098315 DOI: 10.1038/Nsmb.3051 |
0.583 |
|
| 2015 |
Hallen MA, Gainza P, Donald BR. Compact representation of continuous energy surfaces for more efficient protein design. Journal of Chemical Theory and Computation. 11: 2292-2306. PMID 26089744 DOI: 10.1021/Ct501031M |
0.331 |
|
| 2015 |
Roberts KE, Donald BR. Improved energy bound accuracy enhances the efficiency of continuous protein design. Proteins. 83: 1151-64. PMID 25846627 DOI: 10.1002/Prot.24808 |
0.488 |
|
| 2015 |
Martin JW, Zhou P, Donald BR. Systematic solution to homo-oligomeric structures determined by NMR. Proteins. 83: 651-61. PMID 25620116 DOI: 10.1002/Prot.24768 |
0.468 |
|
| 2015 |
Reeve SM, Gainza P, Frey KM, Georgiev I, Donald BR, Anderson AC. Protein design algorithms predict viable resistance to an experimental antifolate. Proceedings of the National Academy of Sciences of the United States of America. 112: 749-54. PMID 25552560 DOI: 10.1073/Pnas.1411548112 |
0.799 |
|
| 2015 |
Qi Y, Martin JW, Yan A, Thelot F, Donald BR, Oas TG. Visualizing the Inter-Domain Motions of a Pathogenic Protein using Sparse RDC Data Biophysical Journal. 108: 58a. DOI: 10.1016/J.Bpj.2014.11.353 |
0.791 |
|
| 2015 |
Jou JD, Jain S, Georgiev I, Donald BR. BWM∗: A novel, provable, ensemble-based dynamic programming algorithm for sparse approximations of computational protein design Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9029: 154-166. DOI: 10.1007/978-3-319-16706-0_16 |
0.621 |
|
| 2015 |
Hallen MA, Donald BR. COMETS (Constrained optimization of multistate energies by tree search): A provable and efficient algorithm to optimize binding affinity and specificity with respect to sequence Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9029: 122-135. DOI: 10.1007/978-3-319-16706-0_14 |
0.331 |
|
| 2014 |
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, ... ... Donald BR, et al. Enhanced potency of a broadly neutralizing HIV-1 antibody in vitro improves protection against lentiviral infection in vivo. Journal of Virology. 88: 12669-82. PMID 25142607 DOI: 10.1128/Jvi.02213-14 |
0.551 |
|
| 2014 |
Zhou Y, Xu W, Donald BR, Zeng J. An efficient parallel algorithm for accelerating computational protein design. Bioinformatics (Oxford, England). 30: i255-i263. PMID 24931991 DOI: 10.1093/Bioinformatics/Btu264 |
0.747 |
|
| 2014 |
Hamaguchi K, Tschida KA, Yoon I, Donald BR, Mooney R. Auditory synapses to song premotor neurons are gated off during vocalization in zebra finches. Elife. 3: e01833. PMID 24550254 DOI: 10.7554/Elife.01833 |
0.541 |
|
| 2014 |
Reardon PN, Sage H, Dennison SM, Martin JW, Donald BR, Alam SM, Haynes BF, Spicer LD. Structure of an HIV-1-neutralizing antibody target, the lipid-bound gp41 envelope membrane proximal region trimer. Proceedings of the National Academy of Sciences of the United States of America. 111: 1391-6. PMID 24474763 DOI: 10.1073/Pnas.1309842111 |
0.344 |
|
| 2014 |
Hamaguchi K, Tschida KA, Yoon I, Donald BR, Mooney R. Author response: Auditory synapses to song premotor neurons are gated off during vocalization in zebra finches Elife. DOI: 10.7554/Elife.01833.019 |
0.517 |
|
| 2014 |
Gainza P, Roberts KE, Hallen MA, Donald BR. Computing Conformational Entropy in Antibody Interfaces Biophysical Journal. 106: 438a. DOI: 10.1016/J.Bpj.2013.11.2470 |
0.43 |
|
| 2014 |
Levey CG, Paprotny I, Donald BR. MicroStressBots: Species differentiation in surface micromachined microrobots Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 8336: 66-80. DOI: 10.1007/978-3-642-55134-5_6 |
0.625 |
|
| 2013 |
Yoon I, Hamaguchi K, Borzenets IV, Finkelstein G, Mooney R, Donald BR. Intracellular Neural Recording with Pure Carbon Nanotube Probes. Plos One. 8: e65715. PMID 23840357 DOI: 10.1371/Journal.Pone.0065715 |
0.549 |
|
| 2013 |
Donald BR, Levey CG, Paprotny I, Rus D. Planning and Control for Microassembly of Structures Composed of Stress-Engineered MEMS Microrobots. The International Journal of Robotics Research. 32: 218-246. PMID 23580796 DOI: 10.1177/0278364912467486 |
0.657 |
|
| 2013 |
Gainza P, Roberts KE, Georgiev I, Lilien RH, Keedy DA, Chen CY, Reza F, Anderson AC, Richardson DC, Richardson JS, Donald BR. OSPREY: protein design with ensembles, flexibility, and provable algorithms. Methods in Enzymology. 523: 87-107. PMID 23422427 DOI: 10.1016/B978-0-12-394292-0.00005-9 |
0.826 |
|
| 2013 |
Zeng J, Zhou P, Donald BR. HASH: a program to accurately predict protein Hα shifts from neighboring backbone shifts. Journal of Biomolecular Nmr. 55: 105-18. PMID 23242797 DOI: 10.1007/S10858-012-9693-7 |
0.703 |
|
| 2013 |
Hallen MA, Keedy DA, Donald BR. Dead-end elimination with perturbations (DEEPer): a provable protein design algorithm with continuous sidechain and backbone flexibility. Proteins. 81: 18-39. PMID 22821798 DOI: 10.1002/Prot.24150 |
0.51 |
|
| 2013 |
Tripathy C, Yan AK, Zhou P, Donald BR. Extracting structural information from residual chemical shift anisotropy: Analytic solutions for peptide plane orientations and applications to determine protein structure Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7821: 271-284. DOI: 10.1007/978-3-642-37195-0_25 |
0.832 |
|
| 2013 |
Paprotny I, Levey CG, Wright PK, Donald BR. Turning-rate selective control : A new method for independent control of stress-engineered MEMS microrobots Robotics: Science and Systems. 8: 321-328. |
0.632 |
|
| 2012 |
Keedy DA, Georgiev I, Triplett EB, Donald BR, Richardson DC, Richardson JS. The role of local backrub motions in evolved and designed mutations. Plos Computational Biology. 8: e1002629. PMID 22876172 DOI: 10.1371/Journal.Pcbi.1002629 |
0.689 |
|
| 2012 |
Borzenets IV, Yoon I, Prior MM, Donald BR, Mooney RD, Finkelstein G. Ultra-sharp metal and nanotube-based probes for applications in scanning microscopy and neural recording. Journal of Applied Physics. 111: 74703-747036. PMID 22550361 DOI: 10.1063/1.3702802 |
0.541 |
|
| 2012 |
Roberts KE, Cushing PR, Boisguerin P, Madden DR, Donald BR. Computational design of a PDZ domain peptide inhibitor that rescues CFTR activity. Plos Computational Biology. 8: e1002477. PMID 22532795 DOI: 10.1371/Journal.Pcbi.1002477 |
0.416 |
|
| 2012 |
Gainza P, Roberts KE, Donald BR. Protein design using continuous rotamers. Plos Computational Biology. 8: e1002335. PMID 22279426 DOI: 10.1371/Journal.Pcbi.1002335 |
0.459 |
|
| 2012 |
Tripathy C, Zeng J, Zhou P, Donald BR. Protein loop closure using orientational restraints from NMR data. Proteins. 80: 433-53. PMID 22161780 DOI: 10.1002/Prot.23207 |
0.845 |
|
| 2012 |
Georgiev I, Acharya P, Schmidt S, Li Y, Wycuff D, Ofek G, Doria-Rose N, Luongo T, Yang Y, Zhou T, Donald B, Mascola J, Kwong P. Design of epitope-specific probes for sera analysis and antibody isolation. Retrovirology. 9: 50. DOI: 10.1186/1742-4690-9-S2-P50 |
0.552 |
|
| 2012 |
Borzenets IV, Yoon I, Prior MW, Donald BR, Mooney RD, Finkelstein G. Publisher’s Note: “Ultra-sharp metal and nanotube-based probes for applications in scanning microscopy and neural recording” [J. Appl. Phys. 111, 074703 (2012)] Journal of Applied Physics. 112: 029906. DOI: 10.1063/1.4739526 |
0.534 |
|
| 2011 |
Apaydin MS, Çatay B, Patrick N, Donald BR. NVR-BIP: Nuclear Vector Replacement using Binary Integer Programming for NMR Structure-Based Assignments. The Computer Journal. 54: 708-716. PMID 25580019 DOI: 10.1093/comjnl/bxp120 |
0.411 |
|
| 2011 |
Martin JW, Yan AK, Bailey-Kellogg C, Zhou P, Donald BR. A geometric arrangement algorithm for structure determination of symmetric protein homo-oligomers from NOEs and RDCs. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 1507-23. PMID 22035328 DOI: 10.1089/Cmb.2011.0173 |
0.838 |
|
| 2011 |
Zeng J, Roberts KE, Zhou P, Donald BR. A Bayesian approach for determining protein side-chain rotamer conformations using unassigned NOE data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 1661-79. PMID 21970619 DOI: 10.1089/Cmb.2011.0172 |
0.751 |
|
| 2011 |
Chandola H, Yan AK, Potluri S, Donald BR, Bailey-Kellogg C. NMR structural inference of symmetric homo-oligomers. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 1757-75. PMID 21718128 DOI: 10.1089/Cmb.2010.0327 |
0.817 |
|
| 2011 |
Zeng J, Zhou P, Donald BR. Protein side-chain resonance assignment and NOE assignment using RDC-defined backbones without TOCSY data. Journal of Biomolecular Nmr. 50: 371-95. PMID 21706248 DOI: 10.1007/S10858-011-9522-4 |
0.736 |
|
| 2011 |
Martin JW, Yan AK, Bailey-Kellogg C, Zhou P, Donald BR. A graphical method for analyzing distance restraints using residual dipolar couplings for structure determination of symmetric protein homo-oligomers. Protein Science : a Publication of the Protein Society. 20: 970-85. PMID 21413097 DOI: 10.1002/Pro.620 |
0.818 |
|
| 2011 |
Tripathy C, Zeng J, Zhou P, Donald BR. Protein loop closure using orientational restraints from NMR data Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6577: 483-498. DOI: 10.1007/978-3-642-20036-6_43 |
0.848 |
|
| 2011 |
Roberts KE, Cushing PR, Boisguerin P, Madden DR, Donald BR. Design of protein-protein interactions with a novel ensemble-based scoring algorithm Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6577: 361-376. DOI: 10.1007/978-3-642-20036-6_35 |
0.35 |
|
| 2010 |
Frey KM, Georgiev I, Donald BR, Anderson AC. Predicting resistance mutations using protein design algorithms. Proceedings of the National Academy of Sciences of the United States of America. 107: 13707-12. PMID 20643959 DOI: 10.1073/Pnas.1002162107 |
0.631 |
|
| 2010 |
Yershova A, Tripathy C, Zhou P, Donald BR. Algorithms and analytic solutions using sparse residual dipolar couplings for high-resolution automated protein backbone structure determination by NMR Springer Tracts in Advanced Robotics. 68: 355-372. DOI: 10.1007/978-3-642-17452-0_21 |
0.846 |
|
| 2010 |
Zeng J, Zhou P, Donald BR. A Markov random field framework for protein side-chain resonance assignment Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6044: 550-570. DOI: 10.1007/978-3-642-12683-3_36 |
0.73 |
|
| 2010 |
Donald BR, Levey CG, Paprotny I, Rus D. Simultaneous control of multiple MEMS microrobots Springer Tracts in Advanced Robotics. 57: 69-84. DOI: 10.1007/978-3-642-00312-7_5 |
0.656 |
|
| 2009 |
Donald BR, Martin J. Automated NMR Assignment and Protein Structure Determination using Sparse Dipolar Coupling Constraints. Progress in Nuclear Magnetic Resonance Spectroscopy. 55: 101-127. PMID 20160991 DOI: 10.1016/J.Pnmrs.2008.12.001 |
0.461 |
|
| 2009 |
Zeng J, Boyles J, Tripathy C, Wang L, Yan A, Zhou P, Donald BR. High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations. Journal of Biomolecular Nmr. 45: 265-81. PMID 19711185 DOI: 10.1007/S10858-009-9366-3 |
0.814 |
|
| 2009 |
Chen CY, Georgiev I, Anderson AC, Donald BR. Computational structure-based redesign of enzyme activity. Proceedings of the National Academy of Sciences of the United States of America. 106: 3764-9. PMID 19228942 DOI: 10.1073/Pnas.0900266106 |
0.611 |
|
| 2008 |
Zeng J, Tripathy C, Zhou P, Donald BR. A Hausdorff-based NOE assignment algorithm using protein backbone determined from residual dipolar couplings and rotamer patterns. Computational Systems Bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. 7: 169-81. PMID 19642278 |
0.843 |
|
| 2008 |
Zeng JM, Tripathy C, Zhou P, Donald BR. A HAUSDORFF-BASED NOE ASSIGNMENT ALGORITHM USING PROTEIN BACKBONE DETERMINED FROM RESIDUAL DIPOLAR COUPLINGS AND ROTAMER PATTERNS. Computational Systems Bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. 2008: 169-181. PMID 19122773 |
0.843 |
|
| 2008 |
Georgiev I, Keedy D, Richardson JS, Richardson DC, Donald BR. Algorithm for backrub motions in protein design. Bioinformatics (Oxford, England). 24: i196-204. PMID 18586714 DOI: 10.1093/bioinformatics/btn169 |
0.672 |
|
| 2008 |
Apaydin MS, Conitzer V, Donald BR. Structure-based protein NMR assignments using native structural ensembles. Journal of Biomolecular Nmr. 40: 263-76. PMID 18365752 DOI: 10.1007/S10858-008-9230-X |
0.54 |
|
| 2008 |
Georgiev I, Lilien RH, Donald BR. The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles. Journal of Computational Chemistry. 29: 1527-42. PMID 18293294 DOI: 10.1002/Jcc.20909 |
0.822 |
|
| 2008 |
Donald BR, Levey CG, Paprotny I. Planar microassembly by parallel actuation of MEMS microrobots Journal of Microelectromechanical Systems. 17: 789-808. DOI: 10.1109/Jmems.2008.924251 |
0.685 |
|
| 2008 |
Potluri S, Yan AK, Chou JJ, Donald BR, Bailey-Kellogg C. Extended abstract: Structure determination of symmetric protein complexes by a complete search of symmetry configuration space using NMR distance restraints Springer Tracts in Advanced Robotics. 47: 335-340. DOI: 10.1007/978-3-540-68405-3_21 |
0.793 |
|
| 2007 |
Gorczynski MJ, Grembecka J, Zhou Y, Kong Y, Roudaia L, Douvas MG, Newman M, Bielnicka I, Baber G, Corpora T, Shi J, Sridharan M, Lilien R, Donald BR, Speck NA, et al. Allosteric inhibition of the protein-protein interaction between the leukemia-associated proteins Runx1 and CBFbeta. Chemistry & Biology. 14: 1186-97. PMID 17961830 DOI: 10.1016/J.Chembiol.2007.09.006 |
0.723 |
|
| 2007 |
Georgiev I, Donald BR. Dead-end elimination with backbone flexibility. Bioinformatics (Oxford, England). 23: i185-94. PMID 17646295 DOI: 10.1093/bioinformatics/btm197 |
0.677 |
|
| 2007 |
Potluri S, Yan AK, Donald BR, Bailey-Kellogg C. A complete algorithm to resolve ambiguity for intersubunit NOE assignment in structure determination of symmetric homo-oligomers. Protein Science : a Publication of the Protein Society. 16: 69-81. PMID 17192589 DOI: 10.1110/Ps.062427307 |
0.827 |
|
| 2007 |
Donald BR, Levey CG, McGray CD, Paprotny I, Rus D. A steerable, untethered, 250 × 60 μm MEMS mobile micro-robot Springer Tracts in Advanced Robotics. 28. |
0.626 |
|
| 2006 |
Wang L, Donald BR. A data-driven, systematic search algorithm for structure determination of denatured or disordered proteins. Computational Systems Bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. 67-78. PMID 17369626 |
0.455 |
|
| 2006 |
Stevens BW, Lilien RH, Georgiev I, Donald BR, Anderson AC. Redesigning the PheA domain of gramicidin synthetase leads to a new understanding of the enzyme's mechanism and selectivity. Biochemistry. 45: 15495-504. PMID 17176071 DOI: 10.1021/Bi061788M |
0.77 |
|
| 2006 |
Wang L, Mettu RR, Donald BR. A polynomial-time algorithm for de novo protein backbone structure determination from nuclear magnetic resonance data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 1267-88. PMID 17037958 DOI: 10.1089/Cmb.2006.13.1267 |
0.54 |
|
| 2006 |
Potluri S, Yan AK, Chou JJ, Donald BR, Bailey-Kellogg C. Structure determination of symmetric homo-oligomers by a complete search of symmetry configuration space, using NMR restraints and van der Waals packing. Proteins. 65: 203-19. PMID 16897780 DOI: 10.1002/Prot.21091 |
0.824 |
|
| 2006 |
Georgiev I, Lilien RH, Donald BR. Improved Pruning algorithms and Divide-and-Conquer strategies for Dead-End Elimination, with application to protein design. Bioinformatics (Oxford, England). 22: e174-83. PMID 16873469 DOI: 10.1093/Bioinformatics/Btl220 |
0.829 |
|
| 2006 |
Donald BR, Levey CG, McGray CG, Paprotny I, Rus D. An untethered, electrostatic, globally controllable MEMS micro-robot Journal of Microelectromechanical Systems. 15: 1-15. DOI: 10.1109/Jmems.2005.863697 |
0.656 |
|
| 2006 |
Georgiev I, Lilien RH, Donald BR. A novel minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3909: 530-545. DOI: 10.1007/11732990_44 |
0.82 |
|
| 2005 |
Wang L, Mettu RR, Donald BR. An algebraic geometry approach to protein structure determination from NMR data. Proceedings / Ieee Computational Systems Bioinformatics Conference, Csb. Ieee Computational Systems Bioinformatics Conference. 235-46. PMID 16447981 DOI: 10.1109/CSB.2005.11 |
0.44 |
|
| 2005 |
Wang L, Donald BR. An efficient and accurate algorithm for assigning nuclear overhauser effect restraints using a rotamer library ensemble and residual dipolar couplings. Proceedings / Ieee Computational Systems Bioinformatics Conference, Csb. Ieee Computational Systems Bioinformatics Conference. 189-202. PMID 16447976 DOI: 10.1109/CSB.2005.13 |
0.478 |
|
| 2005 |
Lilien RH, Stevens BW, Anderson AC, Donald BR. A novel ensemble-based scoring and search algorithm for protein redesign and its application to modify the substrate specificity of the gramicidin synthetase a phenylalanine adenylation enzyme. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 12: 740-61. PMID 16108714 DOI: 10.1089/Cmb.2005.12.740 |
0.775 |
|
| 2005 |
Mettu RR, Lilien RH, Donald BR. High-throughput inference of protein-protein interfaces from unassigned NMR data. Bioinformatics (Oxford, England). 21: i292-301. PMID 15961470 DOI: 10.1093/Bioinformatics/Bti1005 |
0.777 |
|
| 2005 |
Yan AK, Langmead CJ, Donald BR. A probability-based similarity measure for saupe alignment tensors with applications to residual dipolar couplings in NMR structural biology International Journal of Robotics Research. 24: 165-182. DOI: 10.1177/0278364905050351 |
0.818 |
|
| 2005 |
Donald BR. Computational and physical modeling challenges in structural molecular biology and proteomics Acm Symposium On Solid Modeling and Applications, Sm. 7. DOI: 10.1145/1060244.1060245 |
0.354 |
|
| 2005 |
Donald BR. Algorithmic challenges in structural molecular biology and proteomics Springer Tracts in Advanced Robotics. 17: 1-10. |
0.355 |
|
| 2004 |
Wang L, Donald BR. Analysis of a systematic search-based algorithm for determining protein backbone structure from a minimum number of residual dipolar couplings. Proceedings / Ieee Computational Systems Bioinformatics Conference, Csb. Ieee Computational Systems Bioinformatics Conference. 319-30. PMID 16448025 |
0.459 |
|
| 2004 |
Langmead CJ, Donald BR. High-throughput 3D structural homology detection via NMR resonance assignment. Proceedings / Ieee Computational Systems Bioinformatics Conference, Csb. Ieee Computational Systems Bioinformatics Conference. 278-89. PMID 16448021 |
0.664 |
|
| 2004 |
Langmead CJ, Yan A, Lilien R, Wang L, Donald BR. A polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 11: 277-98. PMID 15285893 DOI: 10.1089/1066527041410436 |
0.823 |
|
| 2004 |
Wang L, Donald BR. Exact solutions for internuclear vectors and backbone dihedral angles from NH residual dipolar couplings in two media, and their application in a systematic search algorithm for determining protein backbone structure. Journal of Biomolecular Nmr. 29: 223-42. PMID 15213422 DOI: 10.1023/B:Jnmr.0000032552.69386.Ea |
0.434 |
|
| 2004 |
Lilien RH, Bailey-Kellogg C, Anderson AC, Donald BR. A subgroup algorithm to identify cross-rotation peaks consistent with non-crystallographic symmetry. Acta Crystallographica. Section D, Biological Crystallography. 60: 1057-67. PMID 15159565 DOI: 10.1107/S090744490400695X |
0.749 |
|
| 2004 |
Langmead CJ, Donald BR. An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments. Journal of Biomolecular Nmr. 29: 111-38. PMID 15014227 DOI: 10.1023/B:Jnmr.0000019247.89110.E6 |
0.676 |
|
| 2004 |
Lilien RH, Stevens BW, Andersen AC, Donald BR. A novel ensemble-based scoring and search algorithm for protein redesign, and its application to modify the substrate specificity of the gramicidin synthetase a phenylalanine adenylation enzyme Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 8: 46-57. |
0.76 |
|
| 2003 |
Langmead CJ, Donald BR. 3D structural homology detection via unassigned residual dipolar couplings. Proceedings / Ieee Computer Society Bioinformatics Conference. Ieee Computer Society Bioinformatics Conference. 2: 209-17. PMID 16452795 DOI: 10.1109/CSB.2003.1227320 |
0.657 |
|
| 2003 |
Lilien RH, Farid H, Donald BR. Probabilistic disease classification of expression-dependent proteomic data from mass spectrometry of human serum. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 10: 925-46. PMID 14980018 DOI: 10.1089/106652703322756159 |
0.735 |
|
| 2003 |
O'Neil RH, Lilien RH, Donald BR, Stroud RM, Anderson AC. The crystal structure of dihydrofolate reductase-thymidylate synthase from Cryptosporidium hominis reveals a novel architecture for the bifunctional enzyme. The Journal of Eukaryotic Microbiology. 50: 555-6. PMID 14736160 DOI: 10.1111/J.1550-7408.2003.Tb00627.X |
0.718 |
|
| 2003 |
O'Neil RH, Lilien RH, Donald BR, Stroud RM, Anderson AC. Phylogenetic classification of protozoa based on the structure of the linker domain in the bifunctional enzyme, dihydrofolate reductase-thymidylate synthase. The Journal of Biological Chemistry. 278: 52980-7. PMID 14555647 DOI: 10.1074/Jbc.M310328200 |
0.729 |
|
| 2003 |
Langmead CJ, Yan AK, McClung CR, Donald BR. Phase-independent rhythmic analysis of genome-wide expression patterns. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 10: 521-36. PMID 12935342 DOI: 10.1089/10665270360688165 |
0.779 |
|
| 2003 |
Wang L, Mettu RR, Lilien R, Donald BR. An exact algorithm for determining protein backbone structure from NH residual dipolar couplings Proceedings of the 2003 Ieee Bioinformatics Conference, Csb 2003. 611-612. DOI: 10.1109/CSB.2003.1227422 |
0.771 |
|
| 2002 |
Langmead CJ, McClung CR, Donald BR. A maximum entropy algorithm for rhythmic analysis of genome-wide expression patterns. Proceedings / Ieee Computer Society Bioinformatics Conference. Ieee Computer Society Bioinformatics Conference. 1: 237-45. PMID 15838140 DOI: 10.1109/CSB.2002.1039346 |
0.555 |
|
| 2002 |
Donald BR, Lynch K, Rus D. Introduction to the special issue on algorithmic foundations of robotics International Journal of Robotics Research. 21: 177. DOI: 10.1177/027836402320556386 |
0.323 |
|
| 2001 |
Bailey-Kellogg C, Kelley JJ, Lilien R, Donald BR. Physical geometric algorithms for structural molecular biology Proceedings - Ieee International Conference On Robotics and Automation. 1: 940-947. DOI: 10.1109/ROBOT.2001.932671 |
0.772 |
|
| 2001 |
Langmead CJ, Donald BR. Extracting structural information using time-frequency analysis of protein NMR data Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 164-175. |
0.622 |
|
| 2000 |
Bailey-Kellogg C, Widge A, Kelley JJ, Berardi MJ, Bushweller JH, Donald BR. The NOESY Jigsaw: Automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data Journal of Computational Biology. 7: 537-558. PMID 11108478 DOI: 10.1089/106652700750050934 |
0.513 |
|
| 2000 |
Brown RG, Donald BR. Mobile robot self-localization without explicit landmarks Algorithmica (New York). 26: 515-559. DOI: 10.1007/S004539910023 |
0.307 |
|
| 2000 |
Böhringer KF, Bhatt V, Donald BR, Goldberg K. Algorithms for sensorless manipulation using a vibrating surface Algorithmica (New York). 26: 389-429. DOI: 10.1007/S004539910019 |
0.643 |
|
| 2000 |
Suh JW, Darling RB, Bohringer KF, Donald BR, Baltes H, Kovacs GT. Fully programmable MEMS ciliary actuator arrays for micromanipulation tasks Proceedings - Ieee International Conference On Robotics and Automation. 2: 1101-1108. |
0.597 |
|
| 1999 |
Böhringer KF, Donald BR, MacDonald NC. Programmable Force Fields for Distributed Manipulation, with Applications to MEMS Actuator Arrays and Vibratory Parts Feeders International Journal of Robotics Research. 18: 168-200. DOI: 10.1177/027836499901800205 |
0.639 |
|
| 1999 |
Böhringer KF, Donald BR, Halperin D. On the area bisectors of a polygon Discrete and Computational Geometry. 22: 269-285. DOI: 10.1007/Pl00009460 |
0.645 |
|
| 1995 |
Donald BR, Xavier PG. Provably good approximation algorithms for optimal kinodynamic planning for Cartesian robots and open-chain manipulators Algorithmica. 14: 480-530. DOI: 10.1007/Bf01586637 |
0.35 |
|
| 1995 |
Donald BR, Xavier P. Provably good approximation algorithms for optimal kinodynamic planning: Robots with decoupled dynamics bounds Algorithmica. 14: 443-479. DOI: 10.1007/Bf01586636 |
0.382 |
|
| 1993 |
Donald BR, Pai DK. The Motion of Planar, Compliantly Connected Rigid Bodies in Contact, With Applications to Automatic Fastening The International Journal of Robotics Research. 12: 307-337. DOI: 10.1177/027836499301200401 |
0.341 |
|
| 1993 |
Donald B, Xavier P, Canny J, Reif J. Kinodynamic motion planning Journal of the Acm. 40: 1048-1066. DOI: 10.1145/174147.174150 |
0.585 |
|
| 1990 |
Donald BR. The complexity of planar compliant motion planning under uncertainty Algorithmica. 5: 353-382. DOI: 10.1007/Bf01840394 |
0.302 |
|
| 1987 |
Donald BR. A search algorithm for motion planning with six degrees of freedom Artificial Intelligence. 31: 295-353. DOI: 10.1016/0004-3702(87)90069-5 |
0.364 |
|
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