End-point binding free energy calculation with MM/PBSA and MM/GBSA: strategies and applications in drug design
Molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) and molecular
mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods …
mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods …
Molecular docking: challenges, advances and its use in drug discovery perspective
S Saikia, M Bordoloi - Current drug targets, 2019 - ingentaconnect.com
Molecular docking is a process through which small molecules are docked into the
macromolecular structures for scoring its complementary values at the binding sites. It is a …
macromolecular structures for scoring its complementary values at the binding sites. It is a …
Protein interactions with polymer coatings and biomaterials
Q Wei, T Becherer, S Angioletti‐Uberti… - Angewandte Chemie …, 2014 - Wiley Online Library
Protein adsorption is considered to be the most important factor of the interaction between
polymeric biomaterials and body fluids or tissues. Water‐mediated hydrophobic and …
polymeric biomaterials and body fluids or tissues. Water‐mediated hydrophobic and …
Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches
Entropy effects play an important role in drug–target interactions, but the entropic
contribution to ligand-binding affinity is often neglected by end-point binding free energy …
contribution to ligand-binding affinity is often neglected by end-point binding free energy …
DeepDTAF: a deep learning method to predict protein–ligand binding affinity
Biomolecular recognition between ligand and protein plays an essential role in drug
discovery and development. However, it is extremely time and resource consuming to …
discovery and development. However, it is extremely time and resource consuming to …
H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations
R Anandakrishnan, B Aguilar… - Nucleic acids …, 2012 - academic.oup.com
The accuracy of atomistic biomolecular modeling and simulation studies depend on the
accuracy of the input structures. Preparing these structures for an atomistic modeling task …
accuracy of the input structures. Preparing these structures for an atomistic modeling task …
Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations
The Molecular Mechanics/Poisson− Boltzmann Surface Area (MM/PBSA) and the Molecular
Mechanics/Generalized Born Surface Area (MM/GBSA) methods calculate binding free …
Mechanics/Generalized Born Surface Area (MM/GBSA) methods calculate binding free …
Accuracy and interpretability: The devil and the holy grail. New routes across old boundaries in computational spectroscopy
The past decade has witnessed an increasing interaction between experiment and theory in
the field of molecular spectroscopy. On the computational side, ongoing developments of …
the field of molecular spectroscopy. On the computational side, ongoing developments of …
Improved generalized born solvent model parameters for protein simulations
The generalized Born (GB) model is one of the fastest implicit solvent models, and it has
become widely adopted for Molecular Dynamics (MD) simulations. This speed comes with …
become widely adopted for Molecular Dynamics (MD) simulations. This speed comes with …
Advances and challenges in protein-ligand docking
SY Huang, X Zou - International journal of molecular sciences, 2010 - mdpi.com
Molecular docking is a widely-used computational tool for the study of molecular recognition,
which aims to predict the binding mode and binding affinity of a complex formed by two or …
which aims to predict the binding mode and binding affinity of a complex formed by two or …