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A self-learning algorithm for biased molecular dynamics.
Proc Natl Acad Sci U S A. 2010 Oct 12;107(41):17509-14. doi: 10.1073/pnas.1011511107. Epub 2010 Sep 27.
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Metadynamics in essential coordinates: free energy simulation of conformational changes.
J Phys Chem B. 2007 Mar 29;111(12):3073-6. doi: 10.1021/jp068587c. Epub 2007 Mar 6.
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Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap.
J Chem Phys. 2011 Dec 14;135(22):224504. doi: 10.1063/1.3660208.
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Neural Network and Nearest Neighbor Algorithms for Enhancing Sampling of Molecular Dynamics.
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Continuous metadynamics in essential coordinates as a tool for free energy modelling of conformational changes.
J Mol Model. 2008 Nov;14(11):995-1002. doi: 10.1007/s00894-008-0343-7. Epub 2008 Jul 17.
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Refining Collective Coordinates and Improving Free Energy Representation in Variational Enhanced Sampling.
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Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics.
J Comput Chem. 2009 Aug;30(11):1615-21. doi: 10.1002/jcc.21305.
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Correlation-Based Feature Selection to Identify Functional Dynamics in Proteins.
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Spectral gap optimization of order parameters for sampling complex molecular systems.
Proc Natl Acad Sci U S A. 2016 Mar 15;113(11):2839-44. doi: 10.1073/pnas.1600917113. Epub 2016 Feb 29.

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A Sinking Approach to Explore Arbitrary Areas in Free Energy Landscapes.
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Reaction Coordinates for Conformational Transitions Using Linear Discriminant Analysis on Positions.
J Chem Theory Comput. 2023 Jul 25;19(14):4427-4435. doi: 10.1021/acs.jctc.3c00051. Epub 2023 May 2.
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Collective variable-based enhanced sampling and machine learning.
Eur Phys J B. 2021;94(10):211. doi: 10.1140/epjb/s10051-021-00220-w. Epub 2021 Oct 20.
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Structure-based approaches for drug discovery against .
Comput Struct Biotechnol J. 2021 Jun 24;19:3708-3719. doi: 10.1016/j.csbj.2021.06.034. eCollection 2021.
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DESP: Deep Enhanced Sampling of Proteins' Conformation Spaces Using AI-Inspired Biasing Forces.
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Unsupervised Learning Methods for Molecular Simulation Data.
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Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation.
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Data-Driven Molecular Dynamics: A Multifaceted Challenge.
Pharmaceuticals (Basel). 2020 Sep 18;13(9):253. doi: 10.3390/ph13090253.
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Structural Characterization of the Aurora Kinase B "DFG-flip" Using Metadynamics.
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Prediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling.
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GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.
J Chem Theory Comput. 2008 Mar;4(3):435-47. doi: 10.1021/ct700301q.
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Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics.
Proc Natl Acad Sci U S A. 2010 Mar 16;107(11):4961-6. doi: 10.1073/pnas.0914540107. Epub 2010 Mar 1.
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Computing the viscosity of supercooled liquids.
J Chem Phys. 2009 Jun 14;130(22):224504. doi: 10.1063/1.3139006.
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Gaussian-mixture umbrella sampling.
J Phys Chem B. 2009 Apr 9;113(14):4664-73. doi: 10.1021/jp808381s.
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Advillin folding takes place on a hypersurface of small dimensionality.
Phys Rev Lett. 2008 Nov 14;101(20):208101. doi: 10.1103/PhysRevLett.101.208101. Epub 2008 Nov 10.
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A bias-exchange approach to protein folding.
J Phys Chem B. 2007 May 3;111(17):4553-9. doi: 10.1021/jp067873l. Epub 2007 Apr 10.
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From A to B in free energy space.
J Chem Phys. 2007 Feb 7;126(5):054103. doi: 10.1063/1.2432340.
9
Canonical sampling through velocity rescaling.
J Chem Phys. 2007 Jan 7;126(1):014101. doi: 10.1063/1.2408420.
10

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