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352 Publications visible to you, out of a total of 352
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

Structure-Kinetic-Relationship Reveals the Mechanism of Selectivity of FAK Inhibitors Over PYK2

Abstract

Not specified

Authors: Benedict-Tilman Berger, Marta Amaral, Daria B. Kokh, Ariane Nunes-Alves, Djordje Musil, Timo Heinrich, Martin Schröder, Rebecca Neil, Jing Wang, Iva Navratilova, Joerg Bomke, Jonathan M. Elkins, Susanne Müller, Matthias Frech, Rebecca C. Wade, Stefan Knapp

Date Published: 2020

Publication Type: Journal

Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals

Abstract

Not specified

Authors: Neil J. Bruce, Daniele Narzi, Daniel Trpevski, Siri C. van Keulen, Anu G. Nair, Ursula Röthlisberger, Rebecca C. Wade, Paolo Carloni, Jeanette Hellgren Kotaleski

Date Published: 30th Oct 2019

Publication Type: Journal

Differing Membrane Interactions of Two Highly Similar Drug-Metabolizing Cytochrome P450 Isoforms: CYP 2C9 and CYP 2C19

Abstract

Not specified

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

Date Published: 1st Sep 2019

Publication Type: Journal

Hits and Lead Discovery in the Identification of New Drugs against the Trypanosomatidic Infections

Abstract

Not specified

Authors: Theodora Calogeropoulou, George E. Magoulas, Ina Pöhner, Joanna Panecka-Hofman, Pasquale Linciano, Stefania Ferrari, Nuno Santarem, M. Dolores Jiménez-Antón, Ana Isabel Olías-Molero, José María Alunda, Anabela Cordeiro da Silva, Rebecca C. Wade, Maria Paola Costi

Date Published: 29th Aug 2019

Publication Type: InCollection

KBbox: A Toolbox of Computational Methods for Studying the Kinetics of Molecular Binding

Abstract

Not specified

Authors: Neil J. Bruce, Gaurav K. Ganotra, Stefan Richter, Rebecca C. Wade

Date Published: 5th Aug 2019

Publication Type: Journal

Machine Learning Analysis of τRAMD Trajectories to Decipher Molecular Determinants of Drug-Target Residence Times

Abstract

Not specified

Authors: Daria B. Kokh, Tom Kaufmann, Bastian Kister, Rebecca C. Wade

Date Published: 24th May 2019

Publication Type: Journal

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