@article {2019|2110,
	title = {Effects of all-atom molecular mechanics force fields on amyloid peptide assembly: the case of aβ16{\textendash}22 dimer},
	journal = {Journal of chemical theory and computation},
	volume = {15},
	year = {2019},
	pages = {1440{\textendash}1452},
	author = {Man, Viet Hoang and He, Xibing and Philippe Derreumaux and Ji, Beihong and Xie, Xiang-Qun and Phuong Hoang Nguyen and Wang, Junmei}
}
@article {2016|2027,
	title = {Orientational Dynamics of Water at an Extended Hydrophobic Interface},
	journal = {J Am Chem Soc},
	volume = {138},
	year = {2016},
	month = {May},
	pages = {5551-60},
	abstract = {<p>We report on the orientational dynamics of water at an extended hydrophobic interface with an octadecylsilane self-assembled monolayer on fused silica. The interfacial dangling OH stretch mode is excited with a resonant pump, and its evolution followed in time by a surface-specific, vibrationally resonant, infrared-visible sum-frequency probe. High sensitivity pump-probe anisotropy measurements and isotopic dilution clearly reveal that the decay of the dangling OH stretch excitation is almost entirely due to a jump to a hydrogen-bonded configuration that occurs in 1.61 $\pm$ 0.10 ps. This is more than twice as fast as the jump time from one hydrogen-bonded configuration to another in bulk H2O but about 50\% slower than the reported out-of-plane reorientation at the air/water interface. In contrast, the intrinsic population lifetime of the dangling OH stretch in the absence of such jumps is found to be \&gt;10 ps. Molecular dynamics simulations of air/water and hexane/water interfaces reproduce the fast jump dynamics of interfacial dangling OH with calculated jump times of 1.4 and 1.7 ps for the air and hydrophobic interfaces, respectively. The simulations highlight that while the air/water and hydrophobic/water surfaces exhibit great structural similarities, a small stabilization of the OH groups by the hydrophobic interface produces the pronounced difference in the dynamics of dangling bonds.</p>
},
	doi = {10.1021/jacs.6b01820},
	author = {Xiao, Shunhao and Figge, Florian and Guillaume Stirnemann and Laage, Damien and McGuire, John A}
}
@article {2016|1633,
	title = {Water Determines the Structure and Dynamics of Proteins},
	journal = {Chem. Rev.},
	volume = {116},
	year = {2016},
	pages = {7673{\textendash}7697},
	author = {M-C. Bellissent-Funel and A. Hassanali and M. Havenith and R. Henchman and P. Pohl and Fabio Sterpone and D. van der Spoel and Y. Xu and A. E. Garcia}
}
@article {2014|1380,
	title = {Atomic and Dynamic Insights into the Beneficial Effect of the 1,4-Naphthoquinon-2-yl-L-tryptophan Inhibitor on Alzheimer{\textquoteright}s A beta 1-42 Dimer in Terms of Aggregation and Toxicity},
	journal = {Acs Chem. Neurosci.},
	volume = {5},
	number = {2},
	year = {2014},
	month = {feb},
	pages = {148{\textendash}159},
	author = {Zhang, Tong and Xu, Weixin and Mu, Yuguang and Philippe Derreumaux}
}
@article {2011|1665,
	title = {Community-wide assessment of protein-interface modeling suggests improvements to design methodology.},
	journal = {J. Mol. Biol.},
	volume = {414},
	year = {2011},
	month = {nov},
	pages = {289{\textendash}302},
	abstract = {<p>The CAPRI (Critical Assessment of Predicted Interactions) and CASP (Critical Assessment of protein Structure Prediction) experiments have demonstrated the power of community-wide tests of methodology in assessing the current state of the art and spurring progress in the very challenging areas of protein docking and structure prediction. We sought to bring the power of community-wide experiments to bear on a very challenging protein design problem that provides a complementary but equally fundamental test of current understanding of protein-binding thermodynamics. We have generated a number of designed protein-protein interfaces with very favorable computed binding energies but which do not appear to be formed in experiments, suggesting that there may be important physical chemistry missing in the energy calculations. A total of 28 research groups took up the challenge of determining what is missing: we provided structures of 87 designed complexes and 120 naturally occurring complexes and asked participants to identify energetic contributions and/or structural features that distinguish between the two sets. The community found that electrostatics and solvation terms partially distinguish the designs from the natural complexes, largely due to the nonpolar character of the designed interactions. Beyond this polarity difference, the community found that the designed binding surfaces were, on average, structurally less embedded in the designed monomers, suggesting that backbone conformational rigidity at the designed surface is important for realization of the designed function. These results can be used to improve computational design strategies, but there is still much to be learned; for example, one designed complex, which does form in experiments, was classified by all metrics as a nonbinder.</p>},
	keywords = {Binding Sites, Models, Molecular, Protein Binding, Proteins},
	issn = {1089-8638},
	doi = {10.1016/j.jmb.2011.09.031},
	author = {Fleishman, Sarel J and Whitehead, Timothy A and Strauch, Eva-Maria and Corn, Jacob E and Qin, Sanbo and Zhou, Huan-Xiang and Mitchell, Julie C and Demerdash, Omar N A and Takeda-Shitaka, Mayuko and Terashi, Genki and Moal, Iain H and Li, Xiaofan and Bates, Paul A and Martin Zacharias and Park, Hahnbeom and Ko, Jun-su and Lee, Hasup and Seok, Chaok and Bourquard, Thomas and Bernauer, Julie and Poupon, Anne and Az{\'e}, J{\'e}r{\^o}me and Soner, Seren and Ovali, Sefik Kerem and Ozbek, Pemra and Tal, Nir Ben and Haliloglu, T{\"u}rkan and Hwang, Howook and Vreven, Thom and Pierce, Brian G and Weng, Zhiping and P{\'e}rez-Cano, Laura and Pons, Carles and Fern{\'a}ndez-Recio, Juan and Jiang, Fan and Yang, Feng and Gong, Xinqi and Cao, Libin and Xu, Xianjin and Liu, Bin and Wang, Panwen and Li, Chunhua and Wang, Cunxin and Charles H. Robert and Guharoy, Mainak and Liu, Shiyong and Huang, Yangyu and Li, Lin and Guo, Dachuan and Chen, Ying and Xiao, Yi and London, Nir and Itzhaki, Zohar and Schueler-Furman, Ora and Inbar, Yuval and Potapov, Vladimir and Cohen, Mati and Schreiber, Gideon and Tsuchiya, Yuko and Kanamori, Eiji and Standley, Daron M and Nakamura, Haruki and Kinoshita, Kengo and Driggers, Camden M and Hall, Robert G and Morgan, Jessica L and Hsu, Victor L and Zhan, Jian and Yang, Yuedong and Zhou, Yaoqi and Kastritis, Panagiotis L and Bonvin, Alexandre M J J and Zhang, Weiyi and Camacho, Carlos J and Kilambi, Krishna P and Sircar, Aroop and Gray, Jeffrey J and Ohue, Masahito and Uchikoga, Nobuyuki and Matsuzaki, Yuri and Ishida, Takashi and Akiyama, Yutaka and Khashan, Raed and Bush, Stephen and Fouches, Denis and Tropsha, Alexander and Esquivel-Rodr{\'\i}guez, Juan and Kihara, Daisuke and Stranges, P Benjamin and Jacak, Ron and Kuhlman, Brian and Huang, Sheng-You and Zou, Xiaoqin and Wodak, Shoshana J and Janin, Jo{\"e}l and Baker, David}
}
@article {2011|1966,
	title = {Intrinsic Determinants of A beta(12-24) pH-Dependent Self-Assembly Revealed by Combined Computational and Experimental Studies},
	journal = {Plos One},
	volume = {6},
	number = {9},
	year = {2011},
	month = {sep},
	pages = {e24329},
	doi = {10.1371/journal.pone.0024329},
	author = {Xu, Weixin and Zhang, Ce and Philippe Derreumaux and Graslund, Astrid and Morozova-Roche, Ludmilla and Mu, Yuguang}
}
