Bruce Randall Donald -- Selected Publications
Professor of Computer Science and Biochemistry
Duke University

Books

Selected Recent Publications

• Papers by Topic
  • Structural Molecular Biology and Biochemistry
  • Computational Molecular Biology
  • MicroElectroMechanical Systems (MEMS) and Microrobotics
  • Mobile Robotics
  • Motion Planning and Geometric Algorithms
  • Computer Graphics
  • Computational Geometry
• Indexes of papers listed on
  • Medline
  • DBLP Bibliography Server
  • The Collection of Computer Science Bibliographies
• My C.V. (PDF) (contains a complete list of publications)
• Special Issue of Algorithmica (2000)
• Current Research; Publications prior to 1994; Publications not listed here

Structural Molecular Biology, Biochemistry, & Computational Molecular Biology

• Cover Articles

  

• Indexes and Reviews of Our Papers*

  *This section contains indices and reviews of our papers not written by our group.
  • *Our papers listed on [Medline, DBLP, CCSB]
  • *Data analysis (by S. Aerni and E. Eskin) of the impact of our lab on RECOMB.
  • *Review of our papers on protein design (by SM Lippow & B Tidor). Progress in computational protein design. Curr Opin Biotechnol. 2007 Jul 17; Medline, PMID 17644370.

• Protein Structures

  
  
  
  
  
  
  
  

  	Cover Article, Chemistry & Biology 2007. [Caption]
  	Redesigning the PheA Domain of Gramicidin Synthetase. Biochemistry 2006; 45 (51):15495-15504.
  	Structure of Dihydrofolate Reductase-Thymidylate Synthase from Cryptosporidium hominis. (J. Biol. Chem. 2003).
  	Cover article, J. Eukaryotic Microbiology 2003.
  Complete ensemble of NMR structures of the unphosphorylated human cardiac phospholamban pentamer. PDB ID: 2HYN (Proteins, 2006)

  • Complete ensemble of NMR structures of Unphosphorylated Human Phospholamban Pentamer, (with S. Potluri, A. Yan, J. Chou, and C. Bailey-Kellogg), PDB ID: 2HYN (2006).
  • Crystal structure of Dihydrofolate Reductase-Thymidylate Synthase (DHFR-TS) from Cryptosporidium hominis, (with R. O'Neil, R. Lilien, R. Stroud, and A. Anderson), PDB ID: 1QZF.

• Structural Molecular Biology and Biochemistry

  • "Allosteric Inhibition of the Protein-Protein Interaction Between the Leukemia-Associated Proteins RUNX1 and CBFβ." Chemistry & Biology 2007; 14(10):1186-1197.
    • [Medline, PDF, Supplementary material, PDB structure model, Cover article, Caption, Cover (PDF)]
  • Redesigning the PheA Domain of Gramicidin Synthetase Leads to a New Understanding of the Enzyme's Mechanism and Selectivity (with B. Stevens, R. Lilien, I. Georgiev, and A. Anderson). Biochemistry 2006; 45 (51):15495-15504.
    • [Medline, PDF, Abstract]
  • Structure Determination of Symmetric Homo-oligomers by a Complete Search of Symmetry Configuration Space Using NMR Restraints and van der Waals Packing (with S. Potluri, A. Yan, J. Chou, and C. Bailey-Kellogg). Proteins 2006; 65(1):203-219.
    • [Medline, HTML, PDF, Supplementary materials, Structure (PDB)]
  • 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 (with R. Lilien, B. Stevens, and A. Anderson). Journal of Computational Biology 2005; 12(6-7):740-761.
    • [Medline, PDF]
  • Phylogenetic Classification of Protozoa Based on the Structure of the Linker Domain in the Bifunctional Enzyme, Dihydrofolate Reductase-Thymidylate Synthase (with R. O'Neil, R. Lilien, R. Stroud, and A. Anderson) Journal of Biological Chemistry 2003; 278(52):52980-52987.
    • [Medline, PDF, Full text (at JBC), Structure (PDB)]
  • The Crystal Structure of Dihydrofolate Reductase-Thymidylate Synthase from Cryptosporidium hominis Reveals a Novel Architecture for the Bifunctional Enzyme, (with R. O'Neil, R. Lilien, R. Stroud, and A. Anderson) Journal of Eukaryotic Microbiology 2003; 50(6):555-556. Cover article.
    • [Medline, PDF, Cover illustration (Jpeg)]

• Review/Survey Articles

  • Algorithmic Challenges in Structural Molecular Biology and Proteomics, Plenary lecture at WAFR, Utrecht/Zeist, The Netherlands. July 11-13, 2004. Appears in Springer Tracts in Advanced Robotics (vol. 17), Springer (Berlin) 2005, pp. 1-10.
    • [PDF, HTML]
  • "Physical Geometric Algorithms for Structural Molecular Biology" (with C. Bailey-Kellogg, J. Kelley, and R. Lilien) invited paper at the Special Session on Computational Biology & Chemistry, Proc. International Conference on Robotics and Automation (2001), Seoul, Korea, pp. 940-947.
    • [PostScript, PDF]

• Algorithms in Structural Molecular Biology and Computational Chemistry

  • Algorithm for Backrub Motions in Protein Design (with I. Georgiev, D. Keedy, J. Richardson, and D. Richardson). Bioinformatics 2008; 4(13):i196-i204. Proc. International Conference on Intelligent Systems for Molecular Biology (ISMB), Toronto CA (July, 2008)
    • [PDF, Open access]
  • A Hausdorff-Based NOE Assignment Algorithm Using Protein Backbone Determined from Residual Dipolar Couplings and Rotamer Patterns, (with J. Zeng, C. Tripathy, and P. Zhou). The Computational Systems Bioinformatics Conference (CSB), Stanford CA. (August, 2008) pp. 169-181.
    • [PDF]
  • Structure-Based Protein NMR Assignments using Native Structural Ensembles (with S. Apaydin and V. Conitzer). Journal of Biomolecular NMR 2008; 40(4):263-276. PMID: 18365752.
    • [Medline, PDF]
  • 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 (with I. Georgiev and R. Lilien). Journal of Computational Chemistry 2008;29(10):1527-42. PMID: 1829329
    • [Medline, PDF]
  • Dead-End Elimination with Backbone Flexibility (with I. Georgiev). Proc. International Conference on Intelligent Systems for Molecular Biology (ISMB), Vienna, Austria: July 21-25, 2007. Appears in in Bioinformatics 2007; 23(13):i185-i195.
    • [Medline, PDF, Open Access]
  • A Complete Algorithm to Resolve Ambiguity for Inter-subunit NOE Assignment in Structure Determination of Symmetric Homo-oligomers (with S. Potluri, A. Yan, and C. Bailey-Kellogg). Protein Science 2007; 16(1):69-81.
    • [Medline, PDF]
  • A Polynomial-Time Algorithm for De Novo Protein Backbone Structure Determination from NMR Data (with L. Wang and R. Mettu). Journal of Computational Biology 2006; 13(7): 1276-1288.
    • [Medline, PDF]
  • A Data-Driven, Systematic Search Algorithm for Structure Determination of Denatured or Disordered Proteins (with L. Wang). The Computational Systems Bioinformatics Conference (CSB), Stanford CA. (August, 2006) Pages 67-78. ISBN 1-86094-700-X.
    • Winner of Best Paper Award.
    • [Medline, PDF, Amazon, Imperial College Press]
  • Improved Pruning Algorithms and Divide-and-Conquer Strategies for Dead-End Elimination, with Application to Protein Design (with I. Georgiev and R. Lilien), Proc. International Conference on Intelligent Systems for Molecular Biology (ISMB), Fortaleza, Brazil (2006). Bioinformatics 2006; 22(14):e174-183.
    • [Medline, PDF, Open Access]
  • 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, (with I. Georgiev and R. Lilien). Proceedings of the Tenth Annual International Conference on Research in Computational Molecular Biology (RECOMB), Venice, Italy (April 2-5, 2006). In Springer Berlin, Lecture Notes in Computer Science, RECOMB 2006, LNBI 3909, pp. 530-545, 2006.
    • [Medline, PDF]
  • R. Mettu, R. Lilien, and B. R. Donald. High-Throughput Inference of Protein-Protein Interfaces from Unassigned NMR Data. Bioinformatics 2005; 21(Suppl. 1):i292-i301.
    • [Medline, PDF, Erratum ]
    • Here is the accepted manuscript, which does not contain the error that Bioinformatics introduced in the abstract. The error is corrected in the published Erratum.
  • L. Wang and B. R. Donald. An Efficient and Accurate Algorithm for Assigning Nuclear Overhauser Effect Restraints Using a Rotamer Library Ensemble and Residual Dipolar Couplings. The IEEE Computational Systems Bioinformatics Conference (CSB), Stanford CA. (August, 2005) pp. 189-202.
    • [Medline, PDF ]
  • L. Wang, R. Mettu, and B. R. Donald. An Algebraic Geometry Approach to Protein Backbone Structure Determination from NMR Data. The IEEE Computational Systems Bioinformatics Conference (CSB), Stanford CA. (August, 2005) pp. 235-246.
    • [Medline, PDF ]
  • High-Throughput Inference of Protein-Protein Interfaces from Unassigned NMR Data (with R. Mettu and R. Lilien), Proc. International Conference on Intelligent Systems for Molecular Biology (ISMB), Detroit, MI (2005).
  • 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 (with R. Lilien, B. Stevens, and A. Anderson). Journal of Computational Biology 2005; 12(6-7):740-761.
    • [Medline, PDF]
  • 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 (with L. Wang), Journal of Biomolecular NMR 2004; 29(3):223-242.
    • [Medline, PDF, full text (at JBN)]
  • An Expectation/Maximization Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments (with C. Langmead). Journal of Biomolecular NMR 2004; 29(2):111-138.
    • [Medline, PDF, Full text (at JBN) ]
  • 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 (with R. Lilien, B. Stevens, and A. Anderson). Proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB), San Diego (March 27-31, 2004) pp. 46-57.
    • [PDF]
  • A Subgroup Algorithm to Identify Cross-Rotation Peaks Consistent with Non-Crystallographic Symmetry (with R. Lilien, C. Bailey-Kellogg, and A. Anderson). Acta Crystallographica D: Biological Crystallography 2004; D60, 1057-1067.
    • [Medline, PDF, Full text (at IUCR)]
  • High-Throughput 3D Structural Homology Detection via NMR Resonance Assignment (with C. Langmead). The IEEE Computational Systems Bioinformatics Conference (CSB), Stanford CA, (August, 2004) pp. 278-289.
    • [Medline, PDF]
  • Analysis of a Systematic Search-Based Algorithm for Determining Protein Backbone Structure from a Minimal Number of Residual Dipolar Couplings (with L. Wang). The IEEE Computational Systems Bioinformatics Conference (CSB), Stanford CA (August, 2004) pp. 319-330.
    • [Medline, PDF]

    	Nuclear Vector Replacement.

  • "A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments," (with C. Langmead, A. Yan, R. Lilien, and L. Wang), Journal of Computational Biology 2004; 11(2--3):277-298.
    • [Medline, PDF]
  • A Probability-Based Similarity Measure for Saupe Alignment Tensors with Applications to Residual Dipolar Couplings in NMR Structural Biology (with A. Yan and C. Langmead). The International Journal of Robotics Research Special Issue on Robotics Techniques Applied to Computational Biology, 2005; (29)(2-3):165-182.
    • [PDF]
  • "3D Structural Homology Detection via Unassigned Residual Dipolar Couplings," (with C. Langmead) Proc. IEEE Computational Systems Bioinformatics Conference (CSB), Stanford University, Palo Alto (August 10, 2003) pp. 209-217. ISBN 0-7695-2000-6.
    • [Medline, PDF]
  • "An Exact Algorithm For Determining Protein Backbone Structure From NH Residual Dipolar Couplings,'' (with L. Wang, R. Mettu, and R.Lilien), Proc. IEEE Computational Systems Bioinformatics Conference (CSB), Stanford University, Palo Alto (August 10, 2003) pp. 611-612. ISBN 0-7695-2000-6.
    • Winner of Best Poster Award.
  • "A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments," (with C. Langmead, A. Yan, R. Lilien, and L. Wang), Proc. The Seventh Annual International Conference on Research in Computational Molecular Biology (RECOMB), Berlin (2003) pp. 176-187.
    • [PDF]
  • " Ensembles of active site conformations allow structure-based redesign and drug design," (with A. Anderson, R. Lilien and V. Popov), 225^th American Chemical Society National Meeting, March 23-28, 2003. New Orleans, LA.
  • "Modeling Protein Flexibility for Structure-Based Active Site Redesign", (with R. Lilien and A. Anderson), The Sixth Annual International Conference on Research in Computational Molecular Biology (RECOMB), Washington DC (April 18-21, 2002). In Currents in Computational Molecular Biology, 2002 (ed. L. Florea et al.) pp 122-123.
    • [PDF]
  • "Modeling of Protein Flexibility for Computational Active Site Redesign," (with R. Lilien and A. Anderson) The 16th Annual National MD/PhD Conference, Given Institute, Aspen, Colorado, July 13-15, 2001.
  • "Extracting Structural Information Using Time-Frequency Analysis of Protein NMR Data" (with C. Langmead), Proceedings of The Fifth Annual International Conference on Research in Computational Molecular Biology (RECOMB), Montreal, April 22-25 (2001) pp. 164-175
    • [PDF]
  • "Reducing Mass Degeneracy in SAR by MS (Structure-Activity Relation by Mass Spectrometry) by Stable Isotopic Labeling," (with C. Bailey-Kellogg, J. Kelley, and C. Stein) The Journal of Computational Biology, 8(1):19-36, 2001.
    • [Medline, PDF]
      
    • [The figures look better in this pdfLaTeX reprint]
  • "The NOESY Jigsaw: Automated Protein Secondary Structure and Main-Chain Assignment from Sparse, Unassigned NMR Data," (with C. Bailey-Kellogg, A. Widge, J. Kelley, M. Berardi, and J. Bushweller), The Journal of Computational Biology, 7(3-4) (2000) pp. 537-558.
    • [Medline, PDF]
    • [The figures look better in this pdfLaTeX reprint]
  • "Reducing Mass Degeneracy in SAR by MS (Structure-Activity Relation by Mass Spectrometry) by Stable Isotopic Labeling," (with C. Bailey-Kellogg, J. Kelley, and C. Stein) Proc. the 8th International Conference on Intelligent Systems for Molecular Biology, (August 20-23, 2000) La Jolla, CA (pp. 13-24).
    • [Medline]
  • "Computational Screening Studies for Core-Binding Factor Beta (CBFβ): Use of Multiple Conformations to Model Receptor Flexibility," (with R. Lilien, M. Sridharan, X. Huang, and J. Bushweller), 8th International Conference on Intelligent Systems for Molecular Biology, (August 20-23, 2000) La Jolla, CA.
  • "The NOESY Jigsaw: Automated Protein Secondary Structure and Main-Chain Assignment from Sparse, Unassigned NMR Data," (with C. Bailey-Kellogg, A. Widge, J. Kelley, M. Berardi, and J. Bushweller), The Fourth Annual International Conference on Research in Computational Molecular Biology (RECOMB'2000), Tokyo, Japan, April 8-11, 2000, pp. 33-45.
  
  

• Functional Genomics and Proteomics

  • R. Mettu, R. Lilien, and B. R. Donald. High-Throughput Inference of Protein-Protein Interfaces from Unassigned NMR Data. Bioinformatics 2005; 21(Suppl. 1):i292-i301.
    • [Medline, PDF, Erratum ]
    • Here is the accepted manuscript, which does not contain the error that Bioinformatics introduced in the abstract. The error is corrected in the published Erratum.
  • "Probabilistic Disease Classification of Expression-Dependent Proteomic Data from Mass Spectrometry of Human Serum," (with R. Lilien and H. Farid), Journal of Computational Biology, 10(6) 2003, pp. 925-946.
    • [Medline, PDF]
    • [The figures may look better in this pdfLaTeX reprint]
  • "Phase-Independent Rhythmic Analysis of Genome-Wide Expression Patterns", (with C. Langmead, A. Yan, and C. R. McClung), Journal of Computational Biology 10(3-4) 2003, pp. 521-536.
    • [Medline, PDF]
    • [The figures may look better in this pdfLaTeX reprint]
  • "A Maximum Entropy Algorithm for Rhythmic Analysis of Genome-Wide Expression Patterns," (with C. Langmead and C. R. McClung) Proc. IEEE Computer Society Bioinformatics Conference (CSB), Stanford University, Palo Alto (August 14-16, 2002) pp. 237-245.
    • [Medline, Abstract, PDF]
  • "Phase-Independent Rhythmic Analysis of Genome-Wide Expression Patterns'', (with C. Langmead, T. Yan, and C. R. McClung), The Sixth Annual International Conference on Research in Computational Molecular Biology (RECOMB), Washington DC (April 18-21, 2002). pp. 205-215.
    • [Abstract, PDF]