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Plos Computational Biology|August 8, 2014
Quantitatively characterizing the ligand binding mechanisms of choline binding protein using Markov state model analysisShuo Gu, Daniel-Adriano Silva, Luming Meng, et al.Journal of Chemical Theory and Computation|November 18, 2015
Automatic state partitioning for multibody systems (APM): an efficient algorithm for constructing Markov state models to elucidate conformational dynamics of multibody systemsFu Kit Sheong, Daniel-Adriano Silva, Luming Meng, et al.Nature Communications|June 24, 2014
Dynamic protein conformations preferentially drive energy transfer along the active chain of the photosystem II reaction centreLu Zhang, Daniel-Adriano Silva, Houdao Zhang, et al.The Journal of Chemical Physics|October 5, 2013
Quantitative comparison of alternative methods for coarse-graining biological networksGregory R Bowman, Luming Meng, Xuhui HuangJournal of Computational Chemistry|June 12, 2012
Force field development for cofactors in the photosystem IILu Zhang, Daniel-Adriano Silva, Yijing Yan, et al.The Journal of Physical Chemistry. B|March 11, 2011
Simulating the T-jump-triggered unfolding dynamics of trpzip2 peptide and its time-resolved IR and two-dimensional IR signals using the Markov state model approachWei Zhuang, Raymond Z Cui, Daniel-Adriano Silva, et al.Advances in Experimental Medicine and Biology|January 22, 2014
Application of Markov State Models to simulate long timescale dynamics of biological macromoleculesLin-Tai Da, Fu Kit Sheong, Daniel-Adriano Silva, et al.Plos Computational Biology|June 4, 2011
A role for both conformational selection and induced fit in ligand binding by the LAO proteinDaniel-Adriano Silva, Gregory R Bowman, Alejandro Sosa-Peinado, et al.Plos Computational Biology|July 3, 2015
Structural Model of RNA Polymerase II Elongation Complex with Complete Transcription Bubble Reveals NTP Entry RoutesLu Zhang, Daniel-Adriano Silva, Fátima Pardo-Avila, et al.Science (New York, N.Y.)|July 30, 2011
Initiation complex structure and promoter proofreadingXin Liu, David A Bushnell, Daniel-Adriano Silva, et al.Pageof 44