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The Effect of Force-Field Parameters on Cytochrome P450-Membrane Interactions: Structure and Dynamics

Abstract

Not specified

Authors: Ghulam Mustafa, Prajwal P. Nandekar, Goutam Mukherjee, Neil J. Bruce, Rebecca C. Wade

Date Published: 1st Dec 2020

Publication Type: Journal

RASPD+: Fast Protein-Ligand Binding Free Energy Prediction Using Simplified Physicochemical Features

Abstract (Expand)

The virtual screening of large numbers of compounds against target protein binding sites has become an integral component of drug discovery workflows. This screening is often done by computationally … docking ligands into a protein binding site of interest, but this has the drawback of a large number of poses that must be evaluated to obtain accurate estimates of protein-ligand binding affinity. We here introduce a fast pre-filtering method for ligand prioritization that is based on a set of machine learning models and uses simple pose-invariant physicochemical descriptors of the ligands and the protein binding pocket. Our method, Rapid Screening with Physicochemical Descriptors + machine learning (RASPD+), is trained on PDBbind data and achieves a regression performance that is better than that of the original RASPD method and traditional scoring functions on a range of different test sets without the need for generating ligand poses. Additionally, we use RASPD+ to identify molecular features important for binding affinity and assess the ability of RASPD+ to enrich active molecules from decoys.

Authors: Stefan Holderbach, Lukas Adam, B. Jayaram, Rebecca C. Wade, Goutam Mukherjee

Date Published: 2020

Publication Type: Journal

A Multi-resolution Approach to the Simulation of Protein Complexes in a Membrane Bilayer

Abstract

Not specified

Authors: Goutam Mukherjee, Prajwal Nandekar, Ghulam Mustafa, Stefan Richter, Rebecca C. Wade

Date Published: 2019

Publication Type: InCollection

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