Computational Modeling of the Disulfide Cross-Linking Reaction

Autor: Michael A. Bellucci, Bernhardt L. Trout, Muhammad A Hagras, Gianpaolo Gobbo, Ryan Marek

Publikováno v: The Journal of Physical Chemistry B. 124:9840-9851

Disulfide cross-linking is one of the fundamental covalent bonds that exist prevalently in many biological molecules that is involved in versatile functional activities such as antibody stability, viral assembly, and protein folding. Additionally, it

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ae9cd33ead59c08cf6305cdec53eec65
https://doi.org/10.1021/acs.jpcb.0c07510

Correction to 'A Cloud Computing Platform for Scalable Relative and Absolute Binding Free Energy Prediction: New Opportunities and Challenges for Drug Discovery'

Autor: Zhixiong Lin, Junjie Zou, Shuai Liu, Chunwang Peng, Zhipeng Li, Xiao Wan, Dong Fang, Jian Yin, Gianpaolo Gobbo, Yongpan Chen, Jian Ma, Shuhao Wen, Peiyu Zhang, Mingjun Yang

Publikováno v: Journal of Chemical Information and Modeling. 61:4819-4819

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::0175518afd4d28ba52acf19e056924af
https://doi.org/10.1021/acs.jcim.1c00934

Solubility of paracetamol in ethanol by molecular dynamics using the extended Einstein crystal method and experiments

Autor: Bernhardt L. Trout, Gianpaolo Gobbo, Giovanni Ciccotti, Tharanga K. Wijethunga, Michael A. Bellucci

Publikováno v: The Journal of chemical physics. 150(9)

Li and co-workers [Li et al., J. Chem. Phys. 146, 214110 (2017)] have recently proposed a methodology to compute the solubility of molecular compounds from first principles, using molecular dynamics simulations. We revise and further explore their me

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https://pubmed.ncbi.nlm.nih.gov/30849885

Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps

Autor: Lorenzo Boninsegna, Gianpaolo Gobbo, Cecilia Clementi, Frank Noé

Publikováno v: Boninsegna, L, Gobbo, G, Noe, F & Clementi, C 2015, ' Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps ', Journal of Chemical Theory and Computation, vol. 11, no. 12, pp. 5947-5960 . https://doi.org/10.1021/acs.jctc.5b00749

Identification of the collective coordinates that describe rare events in complex molecular transitions such as protein folding has been a key challenge in the theoretical molecular sciences. In the Diffusion Map approach, one assumes that the molecu

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https://doi.org/10.1021/acs.jctc.5b00749

Absolute transition rates for rare events from dynamical decoupling of reaction variables

Autor: Stefano Baroni, Armin Maleki, Alessandro Laio, Gianpaolo Gobbo

Publikováno v: Gobbo, G, Laio, A, Maleki, A & Baroni, S 2012, ' Absolute Transition Rates for Rare Events from Dynamical Decoupling of Reaction Variables ', Physical Review Letters, vol. 109, no. 15, 150601 . https://doi.org/10.1103/PhysRevLett.109.150601

We introduce a new approach to evaluate transition rates for rare events in complex many-particle systems. Building on a path-integral representation of transition probabilities for Markov processes, the rate is first expressed in terms of a free ene

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b0a1b05ca577d52dc7a3598e78c9d6df
https://pubmed.ncbi.nlm.nih.gov/23102289