Computationally identifying hot spots in protein-DNA binding interfaces using an ensemble approach

[1] Orphanides G(2002)A unified theory of gene expression Cell 108 439-51

[2] Reinberg D(2017)Computational identification of binding energy hot spots in protein-RNA complexes using an ensemble approach Bioinformatics 34 1473-80

[3] Pan Y(2007)Characterization of protein-DNA interactions using surface plasmon resonance spectroscopy with various assay schemes Biochemistry 46 2127-35

[4] Wang Z(1990)Isothermal titration calorimetry Anal Chem 62 950-9

[5] Zhan W(2001)Recent advances in fret: distance determination in protein-DNA complexes Curr Opin Struct Biol 11 201-7

[6] Deng L(2017)Predicting protein-DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver Bioinformatics 34 779-86

[7] Teh HF(2018)PremPDI estimates and interprets the effects of missense mutations on protein-DNA interactions PLoS Comput Biol 14 1006615-82

[8] Peh WY(2010)Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. the accuracy of binding free energy calculations based on molecular dynamics simulations J Chem Inf Model 51 69-6

[9] Su X(2017)mCSM-NA: predicting the effects of mutations on protein–nucleic acids interactions Nucleic Acids Res 45 241-46

[10] Thomsen JS(2019)A feature-based approach to predict hot spots in protein-DNA binding interfaces Brief Bioinform 21 1038-6

[1] Orphanides G(2002)A unified theory of gene expression Cell 108 439-51

[2] Reinberg D(2017)Computational identification of binding energy hot spots in protein-RNA complexes using an ensemble approach Bioinformatics 34 1473-80

[3] Pan Y(2007)Characterization of protein-DNA interactions using surface plasmon resonance spectroscopy with various assay schemes Biochemistry 46 2127-35

[4] Wang Z(1990)Isothermal titration calorimetry Anal Chem 62 950-9

[5] Zhan W(2001)Recent advances in fret: distance determination in protein-DNA complexes Curr Opin Struct Biol 11 201-7

[6] Deng L(2017)Predicting protein-DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver Bioinformatics 34 779-86

[7] Teh HF(2018)PremPDI estimates and interprets the effects of missense mutations on protein-DNA interactions PLoS Comput Biol 14 1006615-82

[8] Peh WY(2010)Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. the accuracy of binding free energy calculations based on molecular dynamics simulations J Chem Inf Model 51 69-6

[9] Su X(2017)mCSM-NA: predicting the effects of mutations on protein–nucleic acids interactions Nucleic Acids Res 45 241-46

[10] Thomsen JS(2019)A feature-based approach to predict hot spots in protein-DNA binding interfaces Brief Bioinform 21 1038-6