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Protocol
Alchemical Free Energy Workflows for the Computation of Protein-Ligand Binding Affinities
Alchemical free energy methods can be used for the efficient computation of relative binding free energies during preclinical drug discovery stages. In recent years, this has been facilitated further by the im...
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Chapter
Pharmaceutical Industry—Academia Cooperation
There has been a long history of fruitful cooperation between academia and the pharmaceutical industry, with the primary beneficiary of this interaction being, of course, the public. Since the middle of the la...
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Protocol
Analyzing GPCR-Ligand Interactions with the Fragment Molecular Orbital (FMO) Method
G-protein-coupled receptors (GPCRs) have enormous physiological and biomedical importance, and therefore it is not surprising that they are the targets of many prescribed drugs. Further progress in GPCR drug d...
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Protocol
Accurate Scoring in Seconds with the Fragment Molecular Orbital and Density-Functional Tight-Binding Methods
The accurate evaluation of receptor-ligand interactions is an essential part of rational drug design. While quantum mechanical (QM) methods have been a promising means by which to achieve this, traditional QM ...
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Protocol
Computational Methods Used in Hit-to-Lead and Lead Optimization Stages of Structure-Based Drug Discovery
GPCR modeling approaches are widely used in the hit-to-lead (H2L) and lead optimization (LO) stages of drug discovery. The aims of these modeling approaches are to predict the 3D structures of the receptor-lig...
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Protocol
Exploring GPCR-Ligand Interactions with the Fragment Molecular Orbital (FMO) Method
The understanding of binding interactions between any protein and a small molecule plays a key role in the rationalization of affinity and selectivity. It is essential for an efficient structure-based drug des...
