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Christopher Bystroff - Publications

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Website:
http://www.bioinfo.rpi.edu/~bystrc/

59 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Shirke AN, Basore D, Holton S, Su A, Baugh E, Butterfoss GL, Makhatadze G, Bystroff C, Gross RA. Influence of surface charge, binding site residues and glycosylation on Thielavia terrestris cutinase biochemical characteristics. Applied Microbiology and Biotechnology. PMID 26758295 DOI: 10.1007/s00253-015-7254-1  1
2015 Shirke AN, Basore D, Butterfoss GL, Bonneau R, Bystroff C, Gross RA. Towards rational thermostabilization of Aspergillus oryzae Cutinase: Insights into catalytic and structural stability. Proteins. PMID 26522152 DOI: 10.1002/prot.24955  1
2015 Huang YM, Banerjee S, Crone DE, Schenkelberg CD, Pitman DJ, Buck PM, Bystroff C. Towards computationally designed self-reporting biosensors using leave-one-out green fluorescent protein. Biochemistry. PMID 26397806 DOI: 10.1021/acs.biochem.5b00786  1
2015 Schenkelberg CD, Bystroff C. InteractiveROSETTA: a graphical user interface for the PyRosetta protein modeling suite. Bioinformatics (Oxford, England). PMID 26315900 DOI: 10.1093/bioinformatics/btv492  1
2015 Pitman DJ, Banerjee S, Macari SJ, Castaldi CA, Crone DE, Bystroff C. Exploring the folding pathway of green fluorescent protein through disulfide engineering. Protein Science : a Publication of the Protein Society. 24: 341-53. PMID 25516354 DOI: 10.1002/pro.2621  1
2014 Rosenman DJ, Huang YM, Xia K, Fraser K, Jones VE, Lamberson CM, Van Roey P, Colón W, Bystroff C. Green-lighting green fluorescent protein: faster and more efficient folding by eliminating a cis-trans peptide isomerization event. Protein Science : a Publication of the Protein Society. 23: 400-10. PMID 24408076 DOI: 10.1002/pro.2421  1
2014 Pitman DJ, Schenkelberg CD, Huang YM, Teets FD, Ditursi D, Bystroff C. Improving computational efficiency and tractability of protein design using a piecemeal approach. A strategy for parallel and distributed protein design. Bioinformatics (Oxford, England). PMID 24371152 DOI: 10.1093/bioinformatics/btt735  1
2013 Huang YM, Bystroff C. Expanded explorations into the optimization of an energy function for protein design. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 10: 1176-87. PMID 24384706 DOI: 10.1109/TCBB.2013.113  1
2013 Xia Y, DiPrimio N, Keppel TR, Vo B, Fraser K, Battaile KP, Egan C, Bystroff C, Lovell S, Weis DD, Anderson JC, Karanicolas J. The designability of protein switches by chemical rescue of structure: mechanisms of inactivation and reactivation. Journal of the American Chemical Society. 135: 18840-9. PMID 24313858 DOI: 10.1021/ja407644b  1
2013 Shong J, Huang YM, Bystroff C, Collins CH. Directed evolution of the quorum-sensing regulator EsaR for increased signal sensitivity. Acs Chemical Biology. 8: 789-95. PMID 23363022 DOI: 10.1021/cb3006402  1
2012 Ramakrishnan V, Srinivasan SP, Salem SM, Matthews SJ, Colón W, Zaki M, Bystroff C. Geofold: topology-based protein unfolding pathways capture the effects of engineered disulfides on kinetic stability. Proteins. 80: 920-34. PMID 22189917 DOI: 10.1002/prot.23249  1
2012 Huang YM, Bystroff C. Exploring objective functions and cross-terms in the optimization of an energy function for protein design 2012 Acm Conference On Bioinformatics, Computational Biology and Biomedicine, Bcb 2012. 155-162. DOI: 10.1145/2382936.2382956  1
2011 Paredes DI, Watters K, Pitman DJ, Bystroff C, Dordick JS. Comparative void-volume analysis of psychrophilic and mesophilic enzymes: Structural bioinformatics of psychrophilic enzymes reveals sources of core flexibility. Bmc Structural Biology. 11: 42. PMID 22013889 DOI: 10.1186/1472-6807-11-42  1
2011 Huang YM, Nayak S, Bystroff C. Quantitative in vivo solubility and reconstitution of truncated circular permutants of green fluorescent protein. Protein Science : a Publication of the Protein Society. 20: 1775-80. PMID 21910151 DOI: 10.1002/pro.735  1
2011 Buck PM, Bystroff C. Constraining local structure can speed up folding by promoting structural polarization of the folding pathway. Protein Science : a Publication of the Protein Society. 20: 959-69. PMID 21413096 DOI: 10.1002/pro.619  1
2010 Reeder PJ, Huang YM, Dordick JS, Bystroff C. A rewired green fluorescent protein: folding and function in a nonsequential, noncircular GFP permutant. Biochemistry. 49: 10773-9. PMID 21090791 DOI: 10.1021/bi100975z  1
2010 Salem S, Zaki MJ, Bystroff C. FlexSnap: flexible non-sequential protein structure alignment. Algorithms For Molecular Biology : Amb. 5: 12. PMID 20047669 DOI: 10.1186/1748-7188-5-12  1
2009 Cole BJ, Bystroff C. Alpha helical crossovers favor right-handed supersecondary structures by kinetic trapping: the phone cord effect in protein folding. Protein Science : a Publication of the Protein Society. 18: 1602-8. PMID 19569186 DOI: 10.1002/pro.182  1
2009 Salem S, Zaki MJ, Bystroff C. Iterative non-sequential protein structural alignment. Journal of Bioinformatics and Computational Biology. 7: 571-96. PMID 19507290 DOI: 10.1142/S0219720009004205  1
2009 Huang YM, Bystroff C. Complementation and reconstitution of fluorescence from circularly permuted and truncated green fluorescent protein. Biochemistry. 48: 929-40. PMID 19140681 DOI: 10.1021/bi802027g  1
2009 Buck PM, Bystroff C. Simulating protein folding initiation sites using an alpha-carbon-only knowledge-based force field. Proteins. 76: 331-42. PMID 19137613 DOI: 10.1002/prot.22348  1
2008 Bystroff C, Webb-Robertson BJ. Pairwise covariance adds little to secondary structure prediction but improves the prediction of non-canonical local structure. Bmc Bioinformatics. 9: 429. PMID 18847485 DOI: 10.1186/1471-2105-9-429  1
2008 Zaki MJ, Bystroff C. Protein structure prediction. Preface. Methods in Molecular Biology (Clifton, N.J.). 413: v-vii. PMID 18453069  1
2008 Bystroff C, Krogh A. Hidden Markov Models for prediction of protein features. Methods in Molecular Biology (Clifton, N.J.). 413: 173-98. PMID 18075166  1
2008 Shinde AV, Bystroff C, Wang C, Vogelezang MG, Vincent PA, Hynes RO, Van De Water L. Identification of the peptide sequences within the EIIIA (EDA) segment of fibronectin that mediate integrin alpha9beta1-dependent cellular activities. The Journal of Biological Chemistry. 283: 2858-70. PMID 17967897 DOI: 10.1074/jbc.M708306200  1
2008 Shentu Z, Al Hasan M, Bystroff C, Zaki MJ. Context shapes: Efficient complementary shape matching for protein-protein docking. Proteins. 70: 1056-73. PMID 17847098 DOI: 10.1002/prot.21600  1
2007 Xia K, Manning M, Hesham H, Lin Q, Bystroff C, Colón W. Identifying the subproteome of kinetically stable proteins via diagonal 2D SDS/PAGE. Proceedings of the National Academy of Sciences of the United States of America. 104: 17329-34. PMID 17956990 DOI: 10.1073/pnas.0705417104  1
2007 Zaki MJ, Bystroff C. Methods of Molecular Biology: Preface Methods in Molecular Biology. 413: v-vii.  1
2006 Huang YM, Bystroff C. Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions. Bioinformatics (Oxford, England). 22: 413-22. PMID 16352653 DOI: 10.1093/bioinformatics/bti828  1
2005 Yuan X, Bystroff C. Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins. Bioinformatics (Oxford, England). 21: 1010-9. PMID 15531601 DOI: 10.1093/bioinformatics/bti128  1
2005 Huang YM, Bystroff C. Improved pairwise alignment of proteins in the Twilight Zone using local structure predictions 2005 Ieee Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts. 243-246. DOI: 10.1109/CSBW.2005.75  1
2005 Girdhar YA, Bystroff C, Akella S. Efficient sampling of protein folding pathways using HMMSTR and probabilistic roadmaps 2005 Ieee Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts. 222-223. DOI: 10.1109/CSBW.2005.59  1
2005 Bystroff C, DeLuca S, McDaniel CN. ECOME: A simple model for an evolving consumption web 2005 Ieee Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts. 260-261. DOI: 10.1109/CSBW.2005.56  1
2004 Bystroff C, Shao Y, Yuan X. Five hierarchical levels of sequence-structure correlation in proteins. Applied Bioinformatics. 3: 97-104. PMID 15693735 DOI: 10.2165/00822942-200403020-00004  1
2004 Hou Y, Hsu W, Lee ML, Bystroff C. Remote homolog detection using local sequence-structure correlations. Proteins. 57: 518-30. PMID 15382242 DOI: 10.1002/prot.20221  1
2004 Zaki MJ, Nadimpally V, Bardhan D, Bystroff C. Predicting protein folding pathways. Bioinformatics (Oxford, England). 20: i386-93. PMID 15262824 DOI: 10.1093/bioinformatics/bth935  1
2003 Yuan X, Shao Y, Bystroff C. Ab initio protein structure prediction using pathway models. Comparative and Functional Genomics. 4: 397-401. PMID 18629080 DOI: 10.1002/cfg.305  1
2003 Zaki MJ, Jin S, Bystroff C. Mining residue contacts in proteins using local structure predictions. Ieee Transactions On Systems, Man, and Cybernetics. Part B, Cybernetics : a Publication of the Ieee Systems, Man, and Cybernetics Society. 33: 789-801. PMID 18238232 DOI: 10.1109/TSMCB.2003.816916  1
2003 Hou Y, Hsu W, Lee ML, Bystroff C. Efficient remote homology detection using local structure. Bioinformatics (Oxford, England). 19: 2294-301. PMID 14630658 DOI: 10.1093/bioinformatics/btg317  1
2003 Shao Y, Bystroff C. Predicting interresidue contacts using templates and pathways. Proteins. 53: 497-502. PMID 14579339 DOI: 10.1002/prot.10539  1
2003 Bystroff C, Garde S. Helix propensities of short peptides: molecular dynamics versus bioinformatics. Proteins. 50: 552-62. PMID 12577261 DOI: 10.1002/prot.10252  1
2002 Bystroff C. MASKER: improved solvent-excluded molecular surface area estimations using Boolean masks. Protein Engineering. 15: 959-65. PMID 12601135  1
2002 Bystroff C, Shao Y. Fully automated ab initio protein structure prediction using I-SITES, HMMSTR and ROSETTA. Bioinformatics (Oxford, England). 18: S54-61. PMID 12169531  1
2002 Bystroff C. Programming hidden Markov models Scientific Programming. 10: 183-184.  1
2001 Bystroff C. An alternative derivation of the equations of motion in torsion space for a branched linear chain. Protein Engineering. 14: 825-8. PMID 11742100  1
2000 Bystroff C, Thorsson V, Baker D. HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins. Journal of Molecular Biology. 301: 173-90. PMID 10926500 DOI: 10.1006/jmbi.2000.3837  1
2000 Thayer EC, Bystroff C, Baker D. Detection of protein coding sequences using a mixture model for local protein amino acid sequence. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 7: 317-27. PMID 10890405 DOI: 10.1089/10665270050081559  1
1999 Simons KT, Ruczinski I, Kooperberg C, Fox BA, Bystroff C, Baker D. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins. 34: 82-95. PMID 10336385 DOI: 10.1002/(SICI)1097-0134(19990101)34:1<82::AID-PROT7>3.0.CO;2-A  1
1998 Yi Q, Bystroff C, Rajagopal P, Klevit RE, Baker D. Prediction and structural characterization of an independently folding substructure in the src SH3 domain. Journal of Molecular Biology. 283: 293-300. PMID 9761691 DOI: 10.1006/jmbi.1998.2072  1
1998 Bystroff C, Baker D. Prediction of local structure in proteins using a library of sequence-structure motifs. Journal of Molecular Biology. 281: 565-77. PMID 9698570 DOI: 10.1006/jmbi.1998.1943  1
1997 Bystroff C, Baker D. Blind predictions of local protein structure in CASP2 targets using the I-sites library. Proteins. 167-71. PMID 9485508 DOI: 10.1002/(SICI)1097-0134(1997)1+<167::AID-PROT21>3.0.CO;2-L  1
1997 Han KF, Bystroff C, Baker D. Three-dimensional structures and contexts associated with recurrent amino acid sequence patterns. Protein Science : a Publication of the Protein Society. 6: 1587-90. PMID 9232660 DOI: 10.1002/pro.5560060723  1
1996 Bystroff C, Simons KT, Han KF, Baker D. Local sequence-structure correlations in proteins. Current Opinion in Biotechnology. 7: 417-21. PMID 8768900 DOI: 10.1016/S0958-1669(96)80117-0  1
1994 McGrath ME, Erpel T, Bystroff C, Fletterick RJ. Macromolecular chelation as an improved mechanism of protease inhibition: structure of the ecotin-trypsin complex. The Embo Journal. 13: 1502-7. PMID 8156987  1
1993 Bystroff C, Baker D, Fletterick RJ, Agard DA. PRISM: application to the solution of two protein structures. Acta Crystallographica. Section D, Biological Crystallography. 49: 440-8. PMID 15299503 DOI: 10.1107/S0907444993004020  1
1993 Baker D, Bystroff C, Fletterick RJ, Agard DA. PRISM: topologically constrained phased refinement for macromolecular crystallography. Acta Crystallographica. Section D, Biological Crystallography. 49: 429-39. PMID 15299502 DOI: 10.1107/S0907444993004032  1
1992 Goddette DW, Paech C, Yang SS, Mielenz JR, Bystroff C, Wilke ME, Fletterick RJ. The crystal structure of the Bacillus lentus alkaline protease, subtilisin BL, at 1.4 A resolution. Journal of Molecular Biology. 228: 580-95. PMID 1453465 DOI: 10.1016/0022-2836(92)90843-9  1
1991 Bystroff C, Kraut J. Crystal structure of unliganded Escherichia coli dihydrofolate reductase. Ligand-induced conformational changes and cooperativity in binding. Biochemistry. 30: 2227-39. PMID 1998681  1
1990 Bystroff C, Oatley SJ, Kraut J. 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. PMID 2185835  1
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