Methods in Molecular Biology - Protein-Ligand Interactions and Drug Design
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Published By Springer US

9781071612088, 9781071612095

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Biased Docking for Protein–Ligand Pose Prediction

Methods in Molecular Biology - Protein-Ligand Interactions and Drug Design ◽

10.1007/978-1-0716-1209-5_3 ◽

2021 ◽

pp. 39-72

Author(s):

Juan Pablo Arcon ◽

Adrián G. Turjanski ◽

Marcelo A. Martí ◽

Stefano Forli

Keyword(s):

Pose Prediction

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Dynamic Docking Using Multicanonical Molecular Dynamics: Simulating Complex Formation at the Atomistic Level

Methods in Molecular Biology - Protein-Ligand Interactions and Drug Design ◽

10.1007/978-1-0716-1209-5_11 ◽

2021 ◽

pp. 187-202

Author(s):

Gert-Jan Bekker ◽

Narutoshi Kamiya

Keyword(s):

Molecular Dynamics ◽

Complex Formation ◽

Dynamic Docking

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Molecular Scaffold Hopping via Holistic Molecular Representation

Methods in Molecular Biology - Protein-Ligand Interactions and Drug Design ◽

10.1007/978-1-0716-1209-5_2 ◽

2021 ◽

pp. 11-35

Author(s):

Francesca Grisoni ◽

Gisbert Schneider

Keyword(s):

Scaffold Hopping ◽

Molecular Scaffold

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Markov State Models to Elucidate Ligand Binding Mechanism

Methods in Molecular Biology - Protein-Ligand Interactions and Drug Design ◽

10.1007/978-1-0716-1209-5_14 ◽

2021 ◽

pp. 239-259

Author(s):

Yunhui Ge ◽

Vincent A. Voelz

Keyword(s):

Ligand Binding ◽

Binding Mechanism ◽

Markov State ◽

Markov State Models ◽

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Fragment-Based Drug Design of Selective HDAC6 Inhibitors

Methods in Molecular Biology - Protein-Ligand Interactions and Drug Design ◽

10.1007/978-1-0716-1209-5_9 ◽

2021 ◽

pp. 155-170

Author(s):

Dusan Ruzic ◽

Nemanja Djokovic ◽

Katarina Nikolic

Keyword(s):

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Negative Image-Based Screening: Rigid Docking Using Cavity Information

Methods in Molecular Biology - Protein-Ligand Interactions and Drug Design ◽

10.1007/978-1-0716-1209-5_7 ◽

2021 ◽

pp. 125-140

Author(s):

Pekka A. Postila ◽

Sami T. Kurkinen ◽

Olli T. Pentikäinen

Keyword(s):

Negative Image ◽

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Binding Mode Prediction and Virtual Screening Applications by Covalent Docking

Methods in Molecular Biology - Protein-Ligand Interactions and Drug Design ◽

10.1007/978-1-0716-1209-5_4 ◽

2021 ◽

pp. 73-88

Author(s):

Andrea Scarpino ◽

György G. Ferenczy ◽

György M. Keserű

Keyword(s):

Virtual Screening ◽

Binding Mode ◽

Binding Mode Prediction ◽

Covalent Docking

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MDock: A Suite for Molecular Inverse Docking and Target Prediction

Methods in Molecular Biology - Protein-Ligand Interactions and Drug Design ◽

10.1007/978-1-0716-1209-5_18 ◽

2021 ◽

pp. 313-322

Author(s):

Zhiwei Ma ◽

Xiaoqin Zou

Keyword(s):

Target Prediction

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Exploiting Water Dynamics for Pharmacophore Screening

Methods in Molecular Biology - Protein-Ligand Interactions and Drug Design ◽

10.1007/978-1-0716-1209-5_13 ◽

2021 ◽

pp. 227-238

Author(s):

David Schaller ◽

Szymon Pach ◽

Marcel Bermudez ◽

Gerhard Wolber

Keyword(s):

Water Dynamics ◽

Pharmacophore Screening

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Free Energy Calculations for Protein–Ligand Binding Prediction

Methods in Molecular Biology - Protein-Ligand Interactions and Drug Design ◽

10.1007/978-1-0716-1209-5_12 ◽

2021 ◽

pp. 203-226

Author(s):

Willem Jespers ◽

Johan Åqvist ◽

Hugo Gutiérrez-de-Terán

Keyword(s):

Free Energy ◽

Ligand Binding ◽

Free Energy Calculations ◽

Binding Prediction ◽

Energy Calculations

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