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The slow but steady rise of binding free energy calculations in drug discovery
The slow but steady rise of binding free energy calculations in drug discovery
Binding free energy calculations are increasingly used in drug discovery research to predict protein-ligand binding affini...
DeepCubist: Molecular Generator for Designing Peptidomimetics based on Complex three-dimensional scaffolds
DeepCubist: Molecular Generator for Designing Peptidomimetics based on Complex three-dimensional scaffolds
Mimicking bioactive conformations of peptide segments involved in the formation of protein-protein interfaces with small m...
Computational investigation of functional water molecules in GPCRs bound to G protein or arrestin
Computational investigation of functional water molecules in GPCRs bound to G protein or arrestin
G protein-coupled receptors (GPCRs) are membrane proteins constituting the largest family of drug targets. The activated G...
Galileo: Three-dimensional searching in large combinatorial fragment spaces on the example of pharmacophores
Galileo: Three-dimensional searching in large combinatorial fragment spaces on the example of pharmacophores
Fragment spaces are an efficient way to model large chemical spaces using a handful of small fragments and a few connectio...
Examining unsupervised ensemble learning using spectroscopy data of organic compounds
Examining unsupervised ensemble learning using spectroscopy data of organic compounds
One solution to the challenge of choosing an appropriate clustering algorithm is to combine different clusterings into a s...
From oncoproteins to spike proteins: the evaluation of intramolecular stability using hydropathic force field
From oncoproteins to spike proteins: the evaluation of intramolecular stability using hydropathic force field
Evaluation of the intramolecular stability of proteins plays a key role in the comprehension of their biological behavior ...
The FMO2 analysis of the ligand-receptor binding energy: the Biscarbene-Gold(I)/DNA G-Quadruplex case study
The FMO2 analysis of the ligand-receptor binding energy: the Biscarbene-Gold(I)/DNA G-Quadruplex case study
In this work, the ab initio fragment molecular orbital (FMO) method was applied to calculate and analyze the binding energ...
Reliable gas-phase tautomer equilibria of drug-like molecule scaffolds and the issue of continuum solvation
Reliable gas-phase tautomer equilibria of drug-like molecule scaffolds and the issue of continuum solvation
Accurate calculation of relative tautomer energies in different environments is a prerequisite to many parameters of relev...
Physicochemical QSAR analysis of hERG inhibition revisited: towards a quantitative potency prediction
Physicochemical QSAR analysis of hERG inhibition revisited: towards a quantitative potency prediction
In an earlier study (Didziapetris R & Lanevskij K (2016). J Comput Aided Mol Des. 30:1175–1188) we collected...
Enabling data-limited chemical bioactivity predictions through deep neural network transfer learning
Enabling data-limited chemical bioactivity predictions through deep neural network transfer learning
The main limitation in developing deep neural network (DNN) models to predict bioactivity properties of chemicals is the l...
Protocol for iterative optimization of modified peptides bound to protein targets
Protocol for iterative optimization of modified peptides bound to protein targets
Peptides are commonly used as therapeutic agents. However, they suffer from easy degradation and instability. Rep...
An overview of the SAMPL8 host–guest binding challenge
An overview of the SAMPL8 host–guest binding challenge
The SAMPL series of challenges aim to focus the community on specific modeling challenges, while testing and hopefully dri...
Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo
Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo
Water plays an important role in mediating protein-ligand interactions. Water rearrangement upon a ligand binding or modif...
Epilogue to the Gerald Maggiora Festschrift: a tribute to an exemplary mentor, colleague, collaborator, and innovator
Epilogue to the Gerald Maggiora Festschrift: a tribute to an exemplary mentor, colleague, collaborator, and innovator
In May 2022, JCAMD published a Special Issue in honor of Gerald (Gerry) Maggiora, whose scientific leadership over many de...
Prot2Prot: a deep learning model for rapid, photorealistic macromolecular visualization
Prot2Prot: a deep learning model for rapid, photorealistic macromolecular visualization
Molecular visualization is a cornerstone of structural biology, providing insights into the form and function of biomolecu...
Covalent docking in CDOCKER
Covalent docking in CDOCKER
Targeted covalent inhibitors (TCIs) are considered to be an important component in the toolbox of drug discovery and about...
FastGrow: on-the-fly growing and its application to DYRK1A
FastGrow: on-the-fly growing and its application to DYRK1A
Fragment-based drug design is an established routine approach in both experimental and computational spheres. Growing frag...
Unveiling the G4-PAMAM capacity to bind and protect Ang-(1-7) bioactive peptide by molecular dynamics simulations
Unveiling the G4-PAMAM capacity to bind and protect Ang-(1-7) bioactive peptide by molecular dynamics simulations
Angiotensin-(1-7) re-balance the Renin-Angiotensin system affected during several pathologies, including the new COVID-19;...
Des3PI: a fragment-based approach to design cyclic peptides targeting protein–protein interactions
Des3PI: a fragment-based approach to design cyclic peptides targeting protein–protein interactions
Protein–protein interactions (PPIs) play crucial roles in many cellular processes and their deregulation often leads...
Modeling receptor flexibility in the structure-based design of KRASG12C inhibitors
Modeling receptor flexibility in the structure-based design of KRASG12C inhibitors
KRAS has long been referred to as an ‘undruggable’ target due to its high affinity for its cognate ligands (GD...
Is the reductionist paradox an Achilles Heel of drug discovery?
Is the reductionist paradox an Achilles Heel of drug discovery?
BrainyQuotes.com. Accessed 30 Aug 2021Maggiora GM (2011) The reductionist paradox: are the laws of chemistry and physics s...