Publications

Bystroff, C. (2022). Cultural Division as a Selective Advantage: Bottom-up Thinking. Mother Pelican, Vol. 18, No. 7, July 2022 Luis T. Gutierrez, Editor. link

Benavides T, Bystroff C. (2022) HMMSTRTM: A hidden Markov model for local struc-ture prediction in globular and membrane associated proteins (in preparation) abstract

Booth R, Jons A, Gong X, Banerjee S, Rye H, Bystroff C, Bondos S. (2022) Immobilization and enhancement of a heterodimeric biosensor in fibrous protein biomaterials Biomacromolecules (Submitted). abstract

Thomas B. Jordan, Kripa N. Nand, Danielle A. Basore,, Ximeng Yuan, Dmitri Zagorevski, Charlie Clarke, Giffin Werner, Zeyuan Guo, Jae Yeon Hwang, Huafeng Wang, Jean-Ju Chung, Christopher Bystroff (2022) In vitro assembly of virus-like particles from bacterial inclusion bodies of chimeric human papillomavirus L1 protein displaying contraceptive antigens. Protein Expression and Purification (submitted) abstract

Danielle A. Basore,, Carolyn M. Barcellona, Thomas B. Jordan, Donna E. Crone, Christopher Bystroff, Scott F. Michael (2022) Engineering a Universal Dengue Virus Vaccine using a Virus-Like Particle Scaffold. Protein Science (submitted) abstract

Bystroff, C. (2021). What Does It Take to Raise the Alarm About the Danger of Overpopulation? Mother Pelican, Vol. 17, No. 8, August 2021 Luis T. Gutierrez, Editor. link

Bystroff, C. (2021). Footprints to singularity: A global population model explains late 20th century slow-down and predicts peak within ten years. PloS one, 16(5), e0247214. abstract

Hwang JY , Nawaz S, Choi J, 4, Wang H , Hussain S , Nawaz M , Lopez-Giraldez F , Dong W , Oh J-N, Bilguvar K, Mane S , Lee C-K, Bystroff C , Lifton RP, Ahmad W, Chung J-J. (2021) Genetic defects in DNAH2 underlie male infertility with multiple morphological abnormalities of the sperm flagella in humans and mice. Frontiers in Cell and Developmental Biology 9. abstract

Koehler Leman, J., Weitzner, B. D., Renfrew, P. D., Lewis, S. M., Moretti, R., Watkins, A. M., ... & Bonneau, R. (2020). Better together: Elements of successful scientific software development in a distributed collaborative community. PLoS computational biology, 16(5), e1007507. abstract

Leman, J. K., Weitzner, B. D., Lewis, S. M., Adolf-Bryfogle, J., Alam, N., Alford, R. F., ... & Bonneau, R. (2020). Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature methods, 17(7), 665-680. abstract

Booth R, Churion K, Bystroff C, & Bondos S. (2020). Binding, Release, and Detection of Ligands by Ultrabithorax Proteinā€Based Materials. The FASEB Journal, 34(S1), 1-1. abstract

Jordan TB, Barcellona C, Basore D, Clark C, Guo Z, Isern S, ... & Xia K. (2019). HPV VLPs as Scaffolds for Vaccine Design. Biophysical Journal, 116(3), 58a. abstract

Kizer, M., Huntress, I. D., Walcott, B., Fraser, K., Bystroff, C., & Wang, X. (2019). The complex between a multi-crossover DNA nanostructure, PX-DNA, and T7 endonuclease I. Biochemistry. Mar 12;58(10):1332-1342. abstract

Bystroff C (2018) Will an anti-sperm contraceptive vaccine gain public acceptance? Obstetrics and Gynecology Reports. Volume 2(3): 1-1. ISSN: 2515-2955 PDF

Hooper WF, Walcott BD, Wang X, Bystroff C. (2018) Fast design of arbitrary length loops in proteins using InteractiveRosetta. BMC Bioinformatics, 19(1), 337. abstract

Bystroff, C. (2018). Intramembranal disulfide cross-linking elucidates the super-quaternary structure of mammalian CatSpers. Reproductive Biology, 18(1), 76-82. abstract

Banerjee S, Schenkelberg CD, Jordan TB, Reimertz JM, Crone EE, Crone DE, & Bystroff C. (2017). Mispacking and the Fitness Landscape of the Green Fluorescent Protein Chromophore Milieu. Biochemistry, 56(5), 736-747. abstract

Schenkelberg CD, Bystroff C. (2016) Protein backbone ensemble generation explores the local structural space of unseen natural homologs. Bioinformatics, 32(10), 1454-1461. 2016 Jan 18:btw001. abstract

Shirke AN, Basore D, Holton S, Su A, Baugh E, Butterfoss GL, Makhatadze G, Bystroff C, Gross RA. (2016) Influence of surface charge, binding site residues and glycosylation on Thielavia terrestris cutinase biochemical characteristics. Applied microbiology and biotechnology. 2016 May 1;100(10):4435-46. abstract

Huang Y-M, Banerjee S, Crone DE, Buck PM, Schenkelberg CD, Pitman DJ & Bystroff C. (2015) Computationally designed biosensors based on leave-one-out green fluorescent protein. Biochemistry 54(40):6263-73. abstract

Shirke AN, Basore D, Butterfoss GL, Bonneau R, Bystroff C, Gross RA (2015) Thermostabilization of Aspergillus oryzae Cutinase using Rational Design Approach. Proteins, Structure, Function and Bioinformatics 84(1), 60-72 abstract

Schenkelberg CD, & Bystroff C. (2015) InteractiveROSETTA: A client graphical user interface for the Py-Rosetta and Rosetta protein modeling suite. Bioinformatics btv492. abstract

Fraser K, Schenkelberg CD, Banerjee S, Thornton C, Lamberson C, Jones V, Choi A, Altshuler R, Dordick JS, and Bystroff C. (2015) "Developing Leave One Out GFP Based Biosensors." Biophysical Journal 108, no. 2 (2015): 328a. abstract

Pitman DJ, Banerjee S, Macari S, Castaldi C, Crone DE, & Bystroff C. (2015) Exploring the folding pathway of green fluorescent protein through disulfide engineering. Protein Science 24:341-353. abstract

Rosenman DJ, Huang Y-M, Xia K, Fraser K, Jones VE, Lamberson CM, Van Roey P & Bystroff C. (2014) Green-lighting Green Fluorescent Protein: Faster and more efficient folding by eliminating a cis-trans peptide isomerization event. Protein Science 23(4):400-410. abstract

Pitman DJ, Schenkelberg CD, Huang Y-M, DiTursi D, Teets FD & Bystroff C. (2013) Improving computational efficiency and tractability of protein design using a piecemeal approach. A strategy for parallel and distributed protein design. Bioinformatics Bioinformatics 2013; doi: 10.1093/bioinformatics/btt735 abstract

Xia Y, DiPrimio N, Keppel T, Vo B, Fraser K, Battaile K, Egan C, Bystroff C, Lovell S, Weis D, Anderson JC, Karanicolas J (2013) The designability of protein switches by chemical rescue of structure: mechanisms of inactivation and reactivation. Journal of the American Chemical Society 135 (50), 18840-18849. abstract

Huang Y-M, & Bystroff C. (2013) Expanded Explorations into the Optimization of an Energy Function for Protein Design. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 26 Sept. 2013. IEEE computer Society Digital Library. IEEE Computer Society, link abstract

Shong J, Huang Y-M, Bystroff C, Collins C. (2013) Directed Evolution of the Quorum-Sensing Regulator EsaR for Increased Signal Sensitivity ACS Chemical Biology 2013 Feb 6. [Epub ahead of print] abstract

Huang Y-M, & Bystroff C. (2012) Exploring objective functions and cross-terms in the optimization of an energy function for protein design. ACM BCB 2012. Orlando FL, Oct 7, 2012. abstract

Crone DE, Huang Y-M, Pitman DJ, Schenkelberg C, Fraser K, Macari S, & Bystroff C. (2012) GFP-based Biosensors State of the Art in Biosensors / Book 1 ISBN 980-953-307-669-5. abstract link PDF

Ramakrishnan V, Srinivasan S, Salem SM, Zaki MJ , Matthews SJ, Colon W, & Bystroff C. (2012) GeoFold: Topology-based protein unfolding pathways capture the effects of engineered disulfides on kinetic stability. Proteins 80(3):920-934. abstract link

Paredes DI, Watters KE, Pitman DJ, Bystroff C, & Dordick JS (2011) Comparative Void-Volume Analysis of Psychrophilic and Mesophilic Enzymes: Structural bioinformatics of psychrophilic enzymes reveals sources of core flexibility BMC Structural Biology 11(1):42 abstract link

Huang Y-M, Nayak S, Bystroff C. (2011) Quantitative in vivo solubility and reconstitution of truncated circular permutants of green fluorescent protein. Protein Science 20(11):1775-80 abstract

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 (online) abstract

Reeder PJ, Huang Y-M, Dordick JS & Bystroff C. (2010) A Rewired Green Fluorescent Protein: Folding and Function in a Nonsequential, Noncircular GFP Permutant. Biochemistry 49(51), 10773-10779. (e-pub). abstract

Salem SM, Zaki MJ, Bystroff C. (2010) FlexSnap: Flexible Non-Sequential Protein Structure Alignment. Algorithms for Molecular Biology Jan 4;5(1):12. abstract

Salem S, Zaki MJ, Bystroff C (2009) Iterative non-sequential protein structural alignment. J Bioinform Comput Biol 7(3):571-96

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 abstract

Huang Y-M & Bystroff C. (2009). Specific complementation and reconstitution of flourescence from a circularly permuted, truncated green fluoresent protein. Biochemistry 48(5):929-40. abstract

Buck P. & Bystroff C. (2008) Simulating protein folding initiation sites using an alpha-carbon-only knowledge-based force field Proteins, Structure, Function and Bioinformatics 76(2):331-342. 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

Yuan, X. & C. Bystroff, Protein Contact Map Prediction. Computational Methods for Protein Structure Prediction and Modeling, 2007: p. 255-277.

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

Bystroff C & Shao Y. (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