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On the Path to Optimal Alchemistry

• Authors : Lundborg, Magnus; Lidmar, Jack, 1968; Hess, Berk

Subjects: Accelerated weight histogram method; Alchemical free energy calculations; Lambda path optimization

• Source: The Protein Journal. 42(5):477-489

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Investigation of protein-ligand interactions using high-throughput all-atom molecular dynamics simulations

• Authors : Buch Mundó, Ignasi; University/Department: Universitat Pompeu Fabra. Departament de Ciències Experimentals i de la Salut; ...

Subjects: Computational biophysics; Molecular dynamics simulations; Distributed computing

• Source: TDX (Tesis Doctorals en Xarxa)

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Molecular modeling of 1-butyl-3-methylimidazolium based ionic liquids for potential applications in the desulfurization of diesel fuel

• Authors : Miranda R. Caudle; Jason E. Thompson; Andrew S. Paluch

Subjects: Ionic liquids; Desulfurization; Molecular simulation

• Source: Journal of Ionic Liquids, Vol 3, Iss 2, Pp 100071- (2023)

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Molecular docking and molecular dynamics simulations reveal the clinical resistance of the gatekeeper mutation V564F of FGFR2 against Infigratinib

• Authors : Guodong Zheng; Wuxia Liu; Qian Zhang

Subjects: FGFR2; Infigratinib; gatekeeper mutation

• Source: Journal of Experimental Nanoscience, Vol 18, Iss 1 (2023)

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Gaussian accelerated molecular dynamics (GaMD): principles and applications.

• Authors : Wang, Jinan; Arantes, Pablo R; Bhattarai, Apurba

Subjects: Networking and Information Technology R&D (NITRD); Generic health relevance; drug binding

• Source: Wiley interdisciplinary reviews. Computational molecular science. 11(5)

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Evaluation of log P, pKa, and log D predictions from the SAMPL7 blind challenge

• Authors : Bergazin, Teresa Danielle; Tielker, Nicolas; Zhang, Yingying

Subjects: Bioengineering; Computational Biology; Computer Simulation

• Source: Journal of Computer-Aided Molecular Design. 35(7)

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Kartograf: An Accurate Graph-Based Atom Mapper For Hybrid Topology Relative Free Energy Calculations

• Authors : Ries, Benjamin; Alibay, Irfan; Henry, Michael M.

Subjects: Free Energy Calculations; Atom Mappings; Cheminformatics

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The Open Free Energy Consortium: Alchemistry for Everyone

• Authors : Gowers, Richard; Alibay, Irfan; Swenson, David W.H.

Subjects: free energy calculations; open source

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The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations

• Authors : Rizzi, Andrea; Jensen, Travis; Slochower, David R

Subjects: Affordable and Clean Energy; Bridged-Ring Compounds; Entropy

• Source: Journal of Computer-Aided Molecular Design. 34(5)

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Assessing the accuracy of octanol–water partition coefficient predictions in the SAMPL6 Part II log P Challenge

• Authors : Işık, Mehtap; Bergazin, Teresa Danielle; Fox, Thomas

Subjects: Bioengineering; Cyclohexanes; Models

• Source: Journal of Computer-Aided Molecular Design. 34(4)

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