AlphaFold2 protein structure prediction: Implications for drug discovery
N Borkakoti, JM Thornton - Current opinion in structural biology, 2023 - Elsevier
The drug discovery process involves designing compounds to selectively interact with their
targets. The majority of therapeutic targets for low molecular weight (small molecule) drugs …
targets. The majority of therapeutic targets for low molecular weight (small molecule) drugs …
[HTML][HTML] A guide to in silico drug design
The drug discovery process is a rocky path that is full of challenges, with the result that very
few candidates progress from hit compound to a commercially available product, often due …
few candidates progress from hit compound to a commercially available product, often due …
Epik: pKa and Protonation State Prediction through Machine Learning
Epik version 7 is a software program that uses machine learning for predicting the p K a
values and protonation state distribution of complex, druglike molecules. Using an ensemble …
values and protonation state distribution of complex, druglike molecules. Using an ensemble …
Alchemical Transformations and Beyond: Recent Advances and Real-World Applications of Free Energy Calculations in Drug Discovery
Computational methods constitute efficient strategies for screening and optimizing potential
drug molecules. A critical factor in this process is the binding affinity between candidate …
drug molecules. A critical factor in this process is the binding affinity between candidate …
Using AlphaFold and experimental structures for the prediction of the structure and binding affinities of GPCR complexes via induced fit docking and free energy …
Free energy perturbation (FEP) remains an indispensable method for computationally
assaying prospective compounds in advance of synthesis. However, before FEP can be …
assaying prospective compounds in advance of synthesis. However, before FEP can be …
Rational and translational implications of D-amino acids for treatment-resistant schizophrenia: from neurobiology to the clinics
A de Bartolomeis, L Vellucci, MC Austin, G De Simone… - Biomolecules, 2022 - mdpi.com
Schizophrenia has been conceptualized as a neurodevelopmental disorder with synaptic
alterations and aberrant cortical–subcortical connections. Antipsychotics are the mainstay of …
alterations and aberrant cortical–subcortical connections. Antipsychotics are the mainstay of …
[HTML][HTML] Quantum chemical package Jaguar: A survey of recent developments and unique features
This paper is dedicated to the quantum chemical package Jaguar, which is commercial
software developed and distributed by Schrödinger, Inc. We discuss Jaguar's scientific …
software developed and distributed by Schrödinger, Inc. We discuss Jaguar's scientific …
Chiral-Controlled Cyclic Chemiluminescence Reactions for the Analysis of Enantiomer Amino Acids
Y Zhong, Y Chen, L Chen, Y Hu, X **ao… - Analytical …, 2023 - ACS Publications
The similarity and complexity of chiral amino acids (AAs) in complex samples remain a
significant challenge in their analysis. In this work, the chiral metal–organic framework …
significant challenge in their analysis. In this work, the chiral metal–organic framework …
FEP Protocol Builder: Optimization of Free Energy Perturbation Protocols Using Active Learning
Significant improvements have been made in the past decade to methods that rapidly and
accurately predict binding affinity through free energy perturbation (FEP) calculations. This …
accurately predict binding affinity through free energy perturbation (FEP) calculations. This …
A Computational Physics-based Approach to Predict Unbound Brain-to-Plasma Partition Coefficient, Kp,uu
M Lawrenz, M Svensson, M Kato… - Journal of Chemical …, 2023 - ACS Publications
The blood–brain barrier (BBB) plays a critical role in preventing harmful endogenous and
exogenous substances from penetrating the brain. Optimal brain penetration of small …
exogenous substances from penetrating the brain. Optimal brain penetration of small …