Chris Bystroff

Prof. Chris Bystroff

Rensselaer Polytechnic Institute, USA



1988 Ph.D., UCSD, La Jolla, USA
1985 M.Sc., UCSD, La Jolla, USA
1983 B.A., Carleton College, USA

Publications (Selected)

  1. Ramakrishnan V, Srinivasan S, Salem SM, Zaki MJ , Matthews SJ, Colon W, & Bystroff C. (2011) GeoFold: Topology-based protein unfolding pathways capture the effects of engineered disulfides on kinetic stability. Proteins (e-pub)
  2. Paredes DI, Watters KE, Pitman DJ, Bystroff C, & Dordick JS (2011) Comparative Void-VolumeAnalysis of Psychrophilic and Mesophilic Enzymes: Structural bioinformatics of psychrophilic enzymes reveals sources of core flexibility BMC Structural Biology 11(1):42.
  3. Huang Y-M, Nayak S, Bystroff C. (2011) Quantitative in vivo solubility and reconstitution of truncated circular permutants of green fluorescent protein. Protein Science20(11), 1771–1940.
  4. Buck PM & Bystroff C (2011) Constraining Local Structure Using Rigid Body Dynamics Can Speed Up Folding By Promoting Structural Polarization Of The Folding Pathway Protein Science 20(6):959-969
  5. Salem SM, Zaki MJ, Bystroff C. (2010) FlexSnap: Flexible Non-Sequential Protein StructureAlignment. Algorithms for Molecular Biology Jan 4;5(1):12.
  6. Reeder PJ, Huang Y-M, Dordick JS & Bystroff C. (2010) A Rewired Green Fluorescent Protein:Folding and Function in a Nonsequential, Noncircular GFP Permutant. Biochemistry49(51),10773-10779.
  7. Cole B & Bystroff C. (2009) Alpha helical crossovers favor right-handed supersecondary structures by a kinetic trapping mechanism. The phone cord effect in protein folding.Protein Science 18(8) 1602 - 1608
  8. Salem, S., Zaki, M.J., Bystroff, C. (2009) Iterative non-sequential protein structural alignment. JBioinform Comput Biol 7(3):571-96
  9. Huang Y-M & Bystroff C. (2009). Specific complementation and reconstitution of flourescencefrom a circularly permuted, truncated green fluoresent protein. Biochemistry48(5):929-40. abstract
  10. Buck P. & Bystroff C. (2008) Simulating protein folding initiation sites using an alpha-carbon­only knowledge-based force field. Proteins, Structure, Function and Bioinformatics 76(2):331-342.
  11. Bystroff C. & Webb-Robertson, B.J. (2008) Pairwise covariance adds little to secondary structureprediction but improves the prediction of non-canonical local structure. BMC Bioinformatics 9:429 (10 October 2008)
  12. Shentu, Z., al Hassan M., Bystroff C., Zaki, M. (2008). Context Shapes: EfficientComplementary Shape Matching for Protein-Protein Docking. Proteins. 70(3):1056-1073
  13. Shinde A., Bystroff C. Wang C., Vincent PA, Hynes RO, van de Water, L. (2008). EIIIA (ED-A), the alternatively spliced segment of fibronectin exhibits cryptic cell adhesive activity to integrin α9β1. J Biol Chem. 283(5):2858-70
  14. Xia K, Manning M, Hesham H, Lin Q, Bystroff C & Colon W. (2007) Identifying theSubproteome of Kinetically Stable Proteins Via Diagonal 2D SDS-PAGE. Proc Nat Acad SciU S A. 104(44):17329-34
  15. Protein Structure Prediction. Series: Methods in Molecular Biology , Vol. 413. Zaki, Mohammed;Bystroff, Christopher (Eds.) 2nd ed., 2007
  16. Bystroff C. & Krogh A. (2007). Hidden Markov Models for Protein Features. Chapter 13 of “Protein Structure Prediction, Methods and Protocols, 2nd Ed” (Zaki M, Bystroff C, eds.) Humana Press.
  17. Yuan X & Bystroff C. (2006). Protein Contact Map Prediction. Chapter 9 of “ComputationalMethods for Protein Structure Prediction and Modeling” (Ying Xu, Dong Xu and Jie Liang, eds.) Springer-Verlag, Heidelberg.
  18. Huang Y-M & Bystroff C. (2006). Improved pairwise alignment of proteins in the Twilight Zoneusing local structure predictions. Bioinformatics 22(4):413-420.
  19. Yuan X & Bystroff C. (2005). Non-sequential Structure-based Alignments Reveal Topology-independent Core Packing Arrangements in Proteins. Bioinformatics 27(7):1010-1019.
  20. Hou Y, Hsu W, Lee ML & Bystroff C. (2004). Remote Homology Detection Using LocalSequence-structure Correlations. Proteins, Structure, Function and Bioinformatics 57(3):518-30.
  21. Zaki MJ, Nadimpally V, Bardhan D, & Bystroff C. (2004). Predicting Protein Folding Pathways. Bioinformatics 20 Suppl. 1, i387-i393.
  22. Bystroff C, Shao Y & Yuan X. (2004). Five heirarchical levels of sequence-structure correlation in proteins. Applied Bioinformatics 3(2):97-104.
  23. Bystroff C & Shao Y. (2004). Modeling Protein Folding Pathways. Practical Bioinformatics(Bujnicki, J. M., Ed.), 97-122, Springer-Verlag, Heidelberg.
  24. Shao Y & Bystroff C. (2003). Predicting inter-residue contacts using templates and pathways. Proteins, Structure, Function and Genetics 53, 497-502.