Publications

Buck P., Bystroff C. (2008) Simulating protein folding initiation sites using an alpha-carbon-only knowledge-based force field Proteins, Structure, Function and Bioinformatics (in review)

Salem S., Zaki M.J., Bystroff C. (2008) Iterative non-sequential protein structural alignment. Journal of Bioinformatics and Computational Biology (in review)

Reeder, P.J., Bystroff, C., and Dordick, J.S. (2008) Re-wiring: Rational Design and Analysis of Protein Topology in Green Fluorescent Protein. In preparation.

Huang Y-M & Bystroff C. (2008). Specific complementation and reconstitution of flourescence from a circularly permuted, truncated green fluoresent protein. Leave-out-out biosensor design. J. Biol. Chem. (in review) abstract

Ramakrishnan V, Salem SM, Zaki MJ , Matthews SJ, Srinivasan S, Colon W, & Bystroff C. (2008) Developing a detailed mechanistic model for protein unfolding. Bioinformatics (in review) abstract

Bystroff C. & Webb-Robertson, B.J. (2008) Pairwise covariance adds little to secondary structure prediction but improves the prediction of non-canonical local structure BMC Bioinformatics 9:429 (10 October 2008) abstract

Shinde A, Bystroff C Wang C, Vogelezang MG, 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 J Biol Chem. 283(5):2858-70 abstract

Shentu, Z., al Hasan, M., Bystroff, C., Zaki, MJ. (2008) Context Shapes: Efficient Complementary Shape Matching for Protein-Protein Docking. Proteins: Structure, Function and Bioinformatics 70(3):1056-1073 abstract

Xia K, Manning M, Hesham H, Lin Q, Bystroff C & Colon W. (2007) Identifying the Subproteome of Kinetically Stable Proteins Via Diagonal 2D SDS-PAGE. Proc Nat Acad Sci U S A. 104(44):17329-34 abstract

Protein Structure Prediction. Series: Methods in Molecular Biology , Vol. 413. Zaki, Mohammed; Bystroff, Christopher (Eds.) 2nd ed., 2007 Link to Humana Press

Bystroff C & Krogh A. (2007). Hidden Markov Models for Predicting Protein Features, in Methods Mol Biol. 2007;413:173-98. abstract

Yuan X & Bystroff C. (2006). Protein Contact Map Prediction, in Computational Methods for Protein Structure Prediction and Modeling (Ying Xu, Dong Xu, eds.) abstract

Huang Y-M & Bystroff C. (2006). Improved pairwise alignment of proteins in the Twilight Zone using local structure predictions. Bioinformatics 22(4):413-420 abstract PDF

Yuan X & Bystroff C. (2005). Non-sequential Structure-based Alignments Reveal Topology-independent Core Packing Arrangements in Proteins. Bioinformatics 21(7):1010-1019 abstract PDF

Girdhar YA, Bystroff C, & Akella S (2005) Efficient sampling of protein folding pathways using HMMSTR and probabilistic roadmaps. Computational Systems Bioinformatics Conference. Workshops and Poster Abstracts. IEEE 8-11 Aug. 2005 pp 222 - 223. abstract

Bystroff C, DeLuca S, & McDaniel CN (2005) ECOME: A simple model for an evolving consumption web. IEEE Computational Systems Bioinformatics Conference - Workshops 8-11 Aug. 2005 pp 260 - 261 abstract

Bystroff C, Shao Y & Yuan X. (2004). Five heirarchical levels of sequence-structure correlation in proteins. Applied Bioinformatics 3(2):97-104 abstract PDF

Zaki MJ, Nadimpally V, Bardhan D, & Bystroff C. (2004). Predicting Protein Folding Pathways. Bioinformatics 20 Suppl. 1, i387-i393. abstract PDF

Hou Y, Hsu W, Lee ML & Bystroff C. (2004). Remote Homology Detection Using Local Sequence-structure Correlations. Proteins 57(3):518-30. abstract PDF

Zaki MJ, Shan J & Bystroff C. (2003). Mining residue contacts in proteins using local structure predictions. IEEE Transactions on Systems, Man and Cybernetics 33, 789-801

Hou Y, Hsu W, Lee ML & Bystroff C. (2003). Efficient Remote Homology Detection Using Local Structure. Bioinformatics 19(17):2294-301. abstract PDF

Shao Y & Bystroff C. (2003a). Predicting inter-residue contacts using templates and pathways. Proteins, Structure, Function and Genetics 53 Suppl 6:497-502. abstract PDF

Shao Y & Bystroff C. (2003b). Modeling Protein Folding Pathways. Practical Bioinformatics (Bujnicki, J. M., Ed.), Springer-Verlag, Heidelberg. abstract PDF

Yuan X, Shao Y & Bystroff C. (2003). Ab initio Protein Structure Prediction Using Pathway Models. Comparative and Functional Genomics 4(4):397-401. abstract PDF

Bystroff C & Garde S. (2003). Helix propensities of short peptides: Molecular dynamics versus bioinformatics. Proteins 50, 552-62. abstract PDF

Bystroff C. (2002). MASKER: Improved solvent excluded molecular surface area estimations using Boolean masks. Protein Eng 15, 959 - 965. abstract PDF

Bystroff C & Shao Y. (2002). Fully automated ab initio protein structure prediction using I-SITES, HMMSTR and ROSETTA. Bioinformatics 18 Suppl 1, S54-61. abstract PDF

Hu J, Shen X, Shao Y, Bystroff C & Zaki MJ. (2002). BIOKDD 2002, Edmonton, Canada abstract PDF

Bystroff C. (2001). An alternative derivation of the equations of motion in torsion space for a branched linear chain. Protein Engineering 14, 825-828. abstract PDF

Zaki MJ & Bystroff C. (2001). Mining Residue Contacts in Proteins. In Data Mining for Scientific and Engineering Applications (R. Grossman, C. Kamath, P. Kegelmeyer, Kumar, V. & Namburu, R., eds.), pp. 141-164. Kluwer Academic Publishers,, Boston, MA. abstract PDF

Bystroff C, Thorsson V & Baker D. (2000). HMMSTR: A hidden markov model for local sequence-structure correlations in proteins. Journal of Molecular Biology 301, 173-90. abstract PDF

Thayer EC, Bystroff C & Baker D. (2000). Detection of protein coding sequences using a mixture model for local protein amino acid sequence. J Comput Biol 7, 317-27. abstract PDF

Zaki MJ, Shan J & Bystroff C. (2000). Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering, Arlington, VA, USA. abstract PDF

Simons KT, Ruczinski I, Kooperberg C, Fox BA, Bystroff C & Baker D. (1999). Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 34, 82-95. abstract PDF

Bystroff C & Baker D. (1998). Prediction of local structure in proteins using a library of sequence-structure motifs. J Mol Biol 281, 565-77. abstract PDF

Yi Q, Bystroff C, Rajagopal P, Klevit RE & Baker D. (1998). Prediction and structural characterization of an independently folding substructure in t he src SH3 domain. J Mol Biol 283, 293-300. abstract PDF

Bystroff C & Baker D. (1997). Blind predictions of local protein structure in CASP2 targets using the I-sites library. Proteins Suppl 1, 167-71. abstract PDF

Han KF, Bystroff C & Baker D. (1997). Three-dimensional structures and contexts associated with recurrent amino acid sequence patterns. Protein Sci 6, 1587-90. abstract

Bystroff C, Simons KT, Han KF & Baker D. (1996). Local sequence-structure correlations in proteins. Curr Opin Biotechnol 7, 417-21. abstract PDF

McGrath ME, Erpel T, Bystroff C & Fletterick RJ. (1994). Macromolecular chelation as an improved mechanism of protease inhibition: structure of the ecotin-trypsin complex. Embo J 13, 1502-7. abstract

Baker D, Bystroff C, Fletterick RJ & Agard DA. (1993). PRISM: topologically constrained phase refinement for macromolecular crystallography. abstract

Bystroff C, Baker D, Fletterick RJ & Agard DA. (1993). PRISM: application to the solution of two protein structures. Acta Crystallographica, Section D (Biological Crystallography) D49, pt.5, 440-8. abstract

Goddette DW, Paech C, Yang SS, Mielenz JR, Bystroff C, Wilke ME & Fletterick RJ. (1992). The crystal structure of the Bacillus lentus alkaline protease, subtilisin BL, at 1.4 A resolution. J Mol Biol 228, 580-95. . abstract

Bystroff C & Kraut J. (1991). Crystal structure of unliganded Escherichia coli dihydrofolate reductase. Ligand-induced conformational changes and cooperativity in binding. Biochemistry 30, 2227-39. abstract

Bystroff C, Oatley SJ & Kraut J. (1990). Crystal structures of Escherichia coli dihydrofolate reductase: the NADP+ holoenzyme and the folate.NADP+ ternary complex. Substrate binding and a model for the transition state. Biochemistry 29, 3263-77. abstract