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Last Name
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Christopher Bystroff

TitleAssociate Professor
InstitutionRensselaer Polytechnic Institute
DepartmentBiology
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     Bibliographic 
     selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. 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. J Am Chem Soc. 2013 Dec 18; 135(50):18840-9.
      View in: PubMed
    2. Huang YM, Bystroff C. Expanded explorations into the optimization of an energy function for protein design. IEEE/ACM Trans Comput Biol Bioinform. 2013 Sep-Oct; 10(5):1176-87.
      View in: PubMed
    3. Shong J, Huang YM, Bystroff C, Collins CH. Directed evolution of the quorum-sensing regulator EsaR for increased signal sensitivity. ACS Chem Biol. 2013 Apr 19; 8(4):789-95.
      View in: PubMed
    4. 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 Struct Biol. 2011; 11:42.
      View in: PubMed
    5. Huang YM, Nayak S, Bystroff C. Quantitative in vivo solubility and reconstitution of truncated circular permutants of green fluorescent protein. Protein Sci. 2011 Nov; 20(11):1775-80.
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    6. Buck PM, Bystroff C. Constraining local structure can speed up folding by promoting structural polarization of the folding pathway. Protein Sci. 2011 Jun; 20(6):959-69.
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    7. Reeder PJ, Huang YM, Dordick JS, Bystroff C. A rewired green fluorescent protein: folding and function in a nonsequential, noncircular GFP permutant. Biochemistry. 2010 Dec 28; 49(51):10773-9.
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    8. Salem S, Zaki MJ, Bystroff C. FlexSnap: flexible non-sequential protein structure alignment. Algorithms Mol Biol. 2010; 5:12.
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    9. Cole BJ, Bystroff C. Alpha helical crossovers favor right-handed supersecondary structures by kinetic trapping: the phone cord effect in protein folding. Protein Sci. 2009 Aug; 18(8):1602-8.
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    10. Buck PM, Bystroff C. Simulating protein folding initiation sites using an alpha-carbon-only knowledge-based force field. Proteins. 2009 Aug 1; 76(2):331-42.
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    11. Salem S, Zaki MJ, Bystroff C. Iterative non-sequential protein structural alignment. J Bioinform Comput Biol. 2009 Jun; 7(3):571-96.
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    12. Huang YM, Bystroff C. Complementation and reconstitution of fluorescence from circularly permuted and truncated green fluorescent protein. Biochemistry. 2009 Feb 10; 48(5):929-40.
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    13. Bystroff C, Webb-Robertson BJ. Pairwise covariance adds little to secondary structure prediction but improves the prediction of non-canonical local structure. BMC Bioinformatics. 2008; 9:429.
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    14. Shentu Z, Al Hasan M, Bystroff C, Zaki MJ. Context shapes: Efficient complementary shape matching for protein-protein docking. Proteins. 2008 Feb 15; 70(3):1056-73.
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    15. Zaki MJ, Bystroff C. Protein structure prediction. Preface. Methods Mol Biol. 2008; 413:v-vii.
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    16. Bystroff C, Krogh A. Hidden Markov Models for prediction of protein features. Methods Mol Biol. 2008; 413:173-98.
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    17. 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. J Biol Chem. 2008 Feb 1; 283(5):2858-70.
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    18. Xia K, Manning M, Hesham H, Lin Q, Bystroff C, Colón W. Identifying the subproteome of kinetically stable proteins via diagonal 2D SDS/PAGE. Proc Natl Acad Sci U S A. 2007 Oct 30; 104(44):17329-34.
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    19. Huang YM, Bystroff C. Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions. Bioinformatics. 2006 Feb 15; 22(4):413-22.
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    20. Hou Y, Hsu W, Lee ML, Bystroff C. Remote homolog detection using local sequence-structure correlations. Proteins. 2004 Nov 15; 57(3):518-30.
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    21. Yuan X, Bystroff C. Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins. Bioinformatics. 2005 Apr 1; 21(7):1010-9.
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    22. Zaki MJ, Nadimpally V, Bardhan D, Bystroff C. Predicting protein folding pathways. Bioinformatics. 2004 Aug 4; 20 Suppl 1:i386-93.
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    23. Bystroff C, Shao Y, Yuan X. Five hierarchical levels of sequence-structure correlation in proteins. Appl Bioinformatics. 2004; 3(2-3):97-104.
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    24. Hou Y, Hsu W, Lee ML, Bystroff C. Efficient remote homology detection using local structure. Bioinformatics. 2003 Nov 22; 19(17):2294-301.
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    25. Bystroff C, Garde S. Helix propensities of short peptides: molecular dynamics versus bioinformatics. Proteins. 2003 Mar 1; 50(4):552-62.
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    26. Shao Y, Bystroff C. Predicting interresidue contacts using templates and pathways. Proteins. 2003; 53 Suppl 6:497-502.
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    27. Yuan X, Shao Y, Bystroff C. Ab initio protein structure prediction using pathway models. Comp Funct Genomics. 2003; 4(4):397-401.
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    28. Zaki MJ, Jin S, Bystroff C. Mining residue contacts in proteins using local structure predictions. IEEE Trans Syst Man Cybern B Cybern. 2003; 33(5):789-801.
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    29. Bystroff C. MASKER: improved solvent-excluded molecular surface area estimations using Boolean masks. Protein Eng. 2002 Dec; 15(12):959-65.
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    30. Bystroff C, Shao Y. Fully automated ab initio protein structure prediction using I-SITES, HMMSTR and ROSETTA. Bioinformatics. 2002; 18 Suppl 1:S54-61.
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    31. Bystroff C. An alternative derivation of the equations of motion in torsion space for a branched linear chain. Protein Eng. 2001 Nov; 14(11):825-8.
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    32. Bystroff C, Thorsson V, Baker D. HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins. J Mol Biol. 2000 Aug 4; 301(1):173-90.
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    33. Thayer EC, Bystroff C, Baker D. Detection of protein coding sequences using a mixture model for local protein amino acid sequence. J Comput Biol. 2000 Feb-Apr; 7(1-2):317-27.
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    34. 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. 1999 Jan 1; 34(1):82-95.
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    35. Bystroff C, Baker D. Prediction of local structure in proteins using a library of sequence-structure motifs. J Mol Biol. 1998 Aug 21; 281(3):565-77.
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    36. Yi Q, Bystroff C, Rajagopal P, Klevit RE, Baker D. Prediction and structural characterization of an independently folding substructure in the src SH3 domain. J Mol Biol. 1998; 283(1):293-300.
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    37. Han KF, Bystroff C, Baker D. Three-dimensional structures and contexts associated with recurrent amino acid sequence patterns. Protein Sci. 1997 Jul; 6(7):1587-90.
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    38. Bystroff C, Baker D. Blind predictions of local protein structure in CASP2 targets using the I-sites library. Proteins. 1997; Suppl 1:167-71.
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    39. Bystroff C, Simons KT, Han KF, Baker D. Local sequence-structure correlations in proteins. Curr Opin Biotechnol. 1996 Aug; 7(4):417-21.
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    40. McGrath ME, Erpel T, Bystroff C, Fletterick RJ. Macromolecular chelation as an improved mechanism of protease inhibition: structure of the ecotin-trypsin complex. EMBO J. 1994 Apr 1; 13(7):1502-7.
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    41. Baker D, Bystroff C, Fletterick RJ, Agard DA. PRISM: topologically constrained phased refinement for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr. 1993 Sep 1; 49(Pt 5):429-39.
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    42. Bystroff C, Baker D, Fletterick RJ, Agard DA. PRISM: application to the solution of two protein structures. Acta Crystallogr D Biol Crystallogr. 1993 Sep 1; 49(Pt 5):440-8.
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    43. 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. J Mol Biol. 1992 Nov 20; 228(2):580-95.
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    44. Bystroff C, Kraut J. Crystal structure of unliganded Escherichia coli dihydrofolate reductase. Ligand-induced conformational changes and cooperativity in binding. Biochemistry. 1991 Feb 26; 30(8):2227-39.
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    45. 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. 1990 Apr 3; 29(13):3263-77.
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