scholarly journals Refining Multi-Scale Enhanced Sampling for Simulating Disordered Protein Conformations

2015 ◽  
Vol 108 (2) ◽  
pp. 161a
Author(s):  
Kuo Hao Lee ◽  
Jianhan Chen
2017 ◽  
Vol 19 (48) ◽  
pp. 32421-32432 ◽  
Author(s):  
Xiaorong Liu ◽  
Jianhan Chen

Efficient coarse-grained (CG) models can be coupled with atomistic force fields to accelerate the sampling of atomistic energy landscapes in the multi-scale enhanced sampling (MSES) framework.


2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Na Liu ◽  
Yue Guo ◽  
Shangbo Ning ◽  
Mojie Duan

Abstract Phosphorylation is one of the most common post-translational modifications. The phosphorylation of the kinase-inducible domain (KID), which is an intrinsically disordered protein (IDP), promotes the folding of KID and binding with the KID-interacting domain (KIX). However, the regulation mechanism of the phosphorylation on KID is still elusive. In this study, the structural ensembles and binding process of pKID and KIX are studied by all-atom enhanced sampling technologies. The results show that more hydrophobic interactions are formed in pKID, which promote the formation of the special hydrophobic residue cluster (HRC). The pre-formed HRC promotes binding to the correct sites of KIX and further lead the folding of pKID. Consequently, a flexible conformational selection model is proposed to describe the binding and folding process of intrinsically disordered proteins. The binding mechanism revealed in this work provides new insights into the dynamic interactions and phosphorylation regulation of proteins.


2017 ◽  
Vol 121 (41) ◽  
pp. 9572-9582 ◽  
Author(s):  
Mattia Bernetti ◽  
Matteo Masetti ◽  
Fabio Pietrucci ◽  
Martin Blackledge ◽  
Malene Ringkjobing Jensen ◽  
...  

2017 ◽  
Vol 113 (3) ◽  
pp. 550-557 ◽  
Author(s):  
Mads Nygaard ◽  
Birthe B. Kragelund ◽  
Elena Papaleo ◽  
Kresten Lindorff-Larsen

2020 ◽  
Author(s):  
Jun Zhang ◽  
Yaokun Lei ◽  
Yi Isaac Yang ◽  
Yi Qin Gao

Molecular simulations are widely applied in the study of chemical and bio-physical systems. However, the<br>accessible timescales of atomistic simulations are limited, and extracting equilibrium properties of systems<br>containing rare events remains challenging. Two distinct strategies are usually adopted in this regard: either<br>sticking to the atomistic level and performing enhanced sampling, or trading details for speed by leveraging<br>coarse-grained models. Although both strategies are promising, either of them, if adopted individually,<br>exhibits severe limitations. In this paper we propose a machine-learning approach to ally both strategies so<br>that simulations on different scales can benefit mutually from their cross-talks: Accurate coarse-grained (CG)<br>models can be inferred from the fine-grained (FG) simulations through deep generative learning; In turn, FG<br>simulations can be boosted by the guidance of CG models via deep reinforcement learning. Our method<br>defines a variational and adaptive training objective which allows end-to-end training of parametric<br>molecular models using deep neural networks. Through multiple experiments, we show that our method is<br>efficient and flexible, and performs well on challenging chemical and bio-molecular systems. <br>


Author(s):  
Jun Zhang ◽  
Yaokun Lei ◽  
Yi Isaac Yang ◽  
Yi Qin Gao

Molecular simulations are widely applied in the study of chemical and bio-physical systems. However, the<br>accessible timescales of atomistic simulations are limited, and extracting equilibrium properties of systems<br>containing rare events remains challenging. Two distinct strategies are usually adopted in this regard: either<br>sticking to the atomistic level and performing enhanced sampling, or trading details for speed by leveraging<br>coarse-grained models. Although both strategies are promising, either of them, if adopted individually,<br>exhibits severe limitations. In this paper we propose a machine-learning approach to ally both strategies so<br>that simulations on different scales can benefit mutually from their cross-talks: Accurate coarse-grained (CG)<br>models can be inferred from the fine-grained (FG) simulations through deep generative learning; In turn, FG<br>simulations can be boosted by the guidance of CG models via deep reinforcement learning. Our method<br>defines a variational and adaptive training objective which allows end-to-end training of parametric<br>molecular models using deep neural networks. Through multiple experiments, we show that our method is<br>efficient and flexible, and performs well on challenging chemical and bio-molecular systems. <br>


2020 ◽  
Author(s):  
Jun Zhang ◽  
Yaokun Lei ◽  
Yi Isaac Yang ◽  
Yi Qin Gao

Molecular simulations are widely applied in the study of chemical and bio-physical systems. However, the<br>accessible timescales of atomistic simulations are limited, and extracting equilibrium properties of systems<br>containing rare events remains challenging. Two distinct strategies are usually adopted in this regard: either<br>sticking to the atomistic level and performing enhanced sampling, or trading details for speed by leveraging<br>coarse-grained models. Although both strategies are promising, either of them, if adopted individually,<br>exhibits severe limitations. In this paper we propose a machine-learning approach to ally both strategies so<br>that simulations on different scales can benefit mutually from their cross-talks: Accurate coarse-grained (CG)<br>models can be inferred from the fine-grained (FG) simulations through deep generative learning; In turn, FG<br>simulations can be boosted by the guidance of CG models via deep reinforcement learning. Our method<br>defines a variational and adaptive training objective which allows end-to-end training of parametric<br>molecular models using deep neural networks. Through multiple experiments, we show that our method is<br>efficient and flexible, and performs well on challenging chemical and bio-molecular systems. <br>


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