Prof. Chris Bystroff

Rensselaer Polytechnic Institute, USA

Email: bystrc@rpi.edu

Qualifications

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.