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Journal Article (22)
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1.Journal ArticlePerformance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset. Journal of Computer-Aided Molecular Design (2019)
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2.Journal ArticleComment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'. eLife 8 (2019)
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3.Journal ArticlePyruvate carboxylase deficiency type A and type C: Characterization of 5 novel pathogenic variants in PC and analysis of the genotype-phenotype correlation. Human Mutation 40 (6), pp. 816 - 827 (2019)
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4.Journal ArticlePredicting kinase inhibitor resistance: Physics-based and data-driven approaches. ACS Central Science 5 (8), pp. 1468 - 1474 (2019)
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5.Journal ArticleAccurate estimation of ligand binding affinity changes upon protein mutation. ACS Central Science 4 (12), pp. 1708 - 1718 (2018)
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6.Journal ArticleConsistent prediction of mutation effect on drug binding in HIV-1 protease using alchemical calculations. Journal of Chemical Theory and Computation 14 (7), pp. 3397 - 3408 (2018)
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7.Journal ArticleUtilizing dipole-dipole cross-correlated relaxation for the measurement of angles between pairs of opposing CαHα-CαHα bonds in anti-parallel β-sheets. Methods 138-139, pp. 85 - 92 (2018)
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8.Journal ArticleResolving the atomistic modes of anle138b inhibitory action on peptide oligomer formation. ACS Chemical Neuroscience 8 (12), pp. 2791 - 2808 (2017)
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9.Journal ArticleAlchemical free energy calculations for nucleotide mutations in protein-DNA complexes. Journal of Chemical Theory and Computation 13 (12), pp. 6275 - 6289 (2017)
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10.Journal Articlepmx Webserver: A user friendly interface for alchemistry. Journal of Chemical Information and Modeling 57 (2), pp. 109 - 114 (2017)
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11.Journal ArticleInsights into the molecular basis for substrate binding and specificity of the wild-type L-arginine/agmatine antiporter AdiC. Proceedings of the National Academy of Sciences of the United States of America 113 (37) (2016)
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12.Journal ArticleAn atomistic view of amyloidogenic self-assembly: Structure and dynamics of heterogeneous conformational states in the pre-nucleation phase. Scientific Reports 6 (2016)
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13.Journal ArticleAccurate and rigorous prediction of the changes in protein free energies in a large-scale mutation scan. Angewandte Chemie-International Edition 55 (26), pp. 7364 - 7368 (2016)
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14.Journal ArticleStructural ensembles of intrinsically disordered proteins depend strongly on force field: A comparison to experiment. Journal of Chemical Theory and Computation 11 (11), pp. 5513 - 5524 (2015)
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15.Journal ArticleImproved validation of IDP ensembles by one-bond Cα-Hα scalar couplings. Journal of Biomolecular NMR 63 (3), pp. 299 - 307 (2015)
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16.Journal ArticlePmx: Automated protein structure and topology generation for alchemical perturbations. Journal of Computational Chemistry 36 (5), pp. 348 - 354 (2015)
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17.Journal ArticlePhosphorylation drives a dynamic switch in serine/arginine-rich proteins. Structure 21 (12), pp. 2162 - 2174 (2013)
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18.Journal ArticleComputational analysis of local membrane properties. Journal of Computer-Aided Molecular Design 27 (10) (2013)
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19.Journal ArticleOptimal superpositioning of flexible molecule ensemble. Biophysical Journal 104 (1), pp. 196 - 207 (2013)
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20.Journal ArticleDriving forces and structural determinants of steric zipper peptide oligomer formation elucidated by atomistic simulations. Journal of Molecular Biology 421 (2-3), pp. 390 - 416 (2012)