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382 Publications visible to you, out of a total of 382
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

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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

Computational ligand superimposition and analysis of protein-ligand interaction fingerprints

Abstract

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Author: Fabian Ormersbach

Date Published: 2020

Publication Type: Bachelor's Thesis

Computational modeling of SERCA interactions with S100A1ct and DWORF fingerprints

Abstract

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Author: Lukas Jarosch

Date Published: 2020

Publication Type: Bachelor's Thesis

Computational approaches to drug design against the folate & biopterin pathways of parasites causing neglected tropical diseases

Abstract

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Author: Ina A. Pöhner

Date Published: 2020

Publication Type: Doctoral Thesis

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

Abstract

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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

From Brazil to Germany: Challenges and Advantages

Abstract

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Author: Ariane Nunes-Alves

Date Published: 16th Sep 2019

Publication Type: Journal

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