Accurate prediction of relative binding affinities of a series of HIV‐1 protease inhibitors using semi‐empirical quantum mechanical charge
Sign Up to like & getrecommendations! Published in 2020 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.26218
Abstract: A major challenge in computer‐aided drug design is the accurate estimation of ligand binding affinity. Here, a new approach that combines the adaptive steered molecular dynamics (ASMD) and partial atomic charges calculated by semi‐empirical quantum… read more here.
Keywords: semi empirical; binding affinities; relative binding; empirical quantum ... See more keywords
Using physics-based pose predictions and free energy perturbation calculations to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Computer-Aided Molecular Design"
DOI: 10.1007/s10822-017-0075-9
Abstract: Computer-aided drug design has become an integral part of drug discovery and development in the pharmaceutical and biotechnology industry, and is nowadays extensively used in the lead identification and lead optimization phases. The drug design… read more here.
Keywords: binding affinities; challenge; relative binding; physics based ... See more keywords
A Benchmark of Electrostatic Method Performance in Relative Binding Free Energy Calculations
Sign Up to like & getrecommendations! Published in 2021 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.0c01424
Abstract: Relative free energy calculations are fast becoming a critical part of early stage pharmaceutical design, making it important to know how to obtain the best performance with these calculations in applications that could span hundreds… read more here.
Keywords: relative binding; energy calculations; binding free; performance ... See more keywords
Relative Binding Free Energy Calculations for Ligands with Diverse Scaffolds with the Alchemical Transfer Method
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.1c01129
Abstract: We present an extension of the alchemical transfer method (ATM) for the estimation of relative binding free energies of molecular complexes applicable to conventional, as well as scaffold-hopping, alchemical transformations. Named ATM-RBFE, the method is… read more here.
Keywords: alchemical transfer; binding free; transfer method; relative binding ... See more keywords
TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal
Sign Up to like & getrecommendations! Published in 2023 at "Journal of Chemical Information and Modeling"
DOI: 10.1021/acs.jcim.2c01596
Abstract: Relative binding free energy (RBFE) calculations are widely used to aid the process of drug discovery. TIES, Thermodynamic Integration with Enhanced Sampling, is a dual-topology approach to RBFE calculations with support for NAMD and OpenMM… read more here.
Keywords: topology; binding free; relative binding; dual topology ... See more keywords
Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations.
Sign Up to like & getrecommendations! Published in 2017 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.7b00564
Abstract: Accurate in silico prediction of protein-ligand binding affinities has been a primary objective of structure-based drug design for decades due to the putative value it would bring to the drug discovery process. However, computational methods… read more here.
Keywords: relative binding; binding free; drug; drug discovery ... See more keywords
Large Scale Study of Ligand–Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Chemical Theory and Computation"
DOI: 10.1021/acs.jctc.1c01288
Abstract: The accurate and reliable prediction of protein–ligand binding affinities can play a central role in the drug discovery process as well as in personalized medicine. Of considerable importance during lead optimization are the alchemical free… read more here.
Keywords: binding free; relative binding; energy calculations; energy ... See more keywords
Efficient Quantification of Lipid Packing Defect Sensing by Amphipathic Peptides: Comparing Martini 2 and 3 with CHARMM36
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Chemical Theory and Computation"
DOI: 10.1021/acs.jctc.2c00222
Abstract: In biological systems, proteins can be attracted to curved or stretched regions of lipid bilayers by sensing hydrophobic defects in the lipid packing on the membrane surface. Here, we present an efficient end-state free energy… read more here.
Keywords: defect sensing; lipid packing; relative binding; packing defect ... See more keywords
Relative Binding Free Energy between Chemically Distant Compounds Using a Bidirectional Nonequilibrium Approach
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Chemical Theory and Computation"
DOI: 10.1021/acs.jctc.2c00295
Abstract: In the context of advanced hit-to-lead drug design based on atomistic molecular dynamics simulations, we propose a dual topology alchemical approach for calculating the relative binding free energy (RBFE) between two chemically distant compounds. The… read more here.
Keywords: topology; binding free; relative binding; free energy ... See more keywords
Assessment of software methods for estimating protein-protein relative binding affinities
Sign Up to like & getrecommendations! Published in 2020 at "PLoS ONE"
DOI: 10.1371/journal.pone.0240573
Abstract: A growing number of computational tools have been developed to accurately and rapidly predict the impact of amino acid mutations on protein-protein relative binding affinities. Such tools have many applications, for example, designing new drugs… read more here.
Keywords: binding affinities; antibody antigen; relative binding;
Relative binding free energy calculations with transformato: A molecular dynamics engine-independent tool
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Molecular Biosciences"
DOI: 10.3389/fmolb.2022.954638
Abstract: We present the software package transformato for the setup of large-scale relative binding free energy calculations. Transformato is written in Python as an open source project (https://github.com/wiederm/transformato); in contrast to comparable tools, it is not… read more here.
Keywords: free energy; molecular dynamics; relative binding; binding free ... See more keywords