Molecular docking: shifting paradigms in drug discovery
L Pinzi, G Rastelli - International journal of molecular sciences, 2019 - mdpi.com
Molecular docking is an established in silico structure-based method widely used in drug
discovery. Docking enables the identification of novel compounds of therapeutic interest …
discovery. Docking enables the identification of novel compounds of therapeutic interest …
A practical guide to machine-learning scoring for structure-based virtual screening
Abstract Structure-based virtual screening (SBVS) via docking has been used to discover
active molecules for a range of therapeutic targets. Chemical and protein data sets that …
active molecules for a range of therapeutic targets. Chemical and protein data sets that …
Protein structure-based drug design: from docking to molecular dynamics
P Śledź, A Caflisch - Current opinion in structural biology, 2018 - Elsevier
Highlights•High-throughput docking of small molecules is very successful in hit identification,
particularly for screening mainly rigid fragments.•Classical force fields with implicit solvent …
particularly for screening mainly rigid fragments.•Classical force fields with implicit solvent …
Protein–ligand docking in the machine-learning era
Molecular docking plays a significant role in early-stage drug discovery, from structure-
based virtual screening (VS) to hit-to-lead optimization, and its capability and predictive …
based virtual screening (VS) to hit-to-lead optimization, and its capability and predictive …
Advances in molecular dynamics simulations and enhanced sampling methods for the study of protein systems
Molecular dynamics (MD) simulation is a rigorous theoretical tool that when used efficiently
could provide reliable answers to questions pertaining to the structure-function relationship …
could provide reliable answers to questions pertaining to the structure-function relationship …
Niosomes: a novel targeted drug delivery system for cancer
M Moghtaderi, K Sedaghatnia, M Bourbour… - Medical Oncology, 2022 - Springer
Recently, nanotechnology is involved in various fields of science, of which medicine is one
of the most obvious. The use of nanoparticles in the process of treating and diagnosing …
of the most obvious. The use of nanoparticles in the process of treating and diagnosing …
Discovery of cryptic allosteric sites using reversed allosteric communication by a combined computational and experimental strategy
Allostery, which is one of the most direct and efficient methods to fine-tune protein functions,
has gained increasing recognition in drug discovery. However, there are several challenges …
has gained increasing recognition in drug discovery. However, there are several challenges …
Predicting the locations of cryptic pockets from single protein structures using the PocketMiner graph neural network
Cryptic pockets expand the scope of drug discovery by enabling targeting of proteins
currently considered undruggable because they lack pockets in their ground state structures …
currently considered undruggable because they lack pockets in their ground state structures …
Investigating cryptic binding sites by molecular dynamics simulations
A Kuzmanic, GR Bowman… - Accounts of chemical …, 2020 - ACS Publications
Conspectus This Account highlights recent advances and discusses major challenges in
investigations of cryptic (hidden) binding sites by molecular simulations. Cryptic binding …
investigations of cryptic (hidden) binding sites by molecular simulations. Cryptic binding …
Drug specificity and affinity are encoded in the probability of cryptic pocket opening in myosin motor domains
The design of compounds that can discriminate between closely related target proteins
remains a central challenge in drug discovery. Specific therapeutics targeting the highly …
remains a central challenge in drug discovery. Specific therapeutics targeting the highly …