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Beware of the generic machine learning-based scoring functions in structure-based virtual screening

Briefings in bioinformatics, 2021-05, Vol.22 (3)

2021

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Discovery of novel TRPV1 modulators through machine learning‐based molecular docking and molecular similarity searching

Chemical biology & drug design, 2023-09, Vol.102 (3), p.409-423

2023

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Assessing How Residual Errors of Scoring Functions Correlate to Ligand Structural Features

International journal of molecular sciences, 2022-11, Vol.23 (23), p.15018

2022

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Machine learning on ligand-residue interaction profiles to significantly improve binding affinity prediction

Briefings in bioinformatics, 2021-09, Vol.22 (5)

2021

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Multipass membrane protein structure prediction using Rosetta

Proteins, structure, function, and bioinformatics, 2006-03, Vol.62 (4), p.1010-1025

2006

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GalaxyDock BP2 score: a hybrid scoring function for accurate protein–ligand docking

Journal of computer-aided molecular design, 2017-07, Vol.31 (7), p.653-666

2017

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DynaDock: A new molecular dynamics-based algorithm for protein-peptide docking including receptor flexibility

Proteins, structure, function, and bioinformatics, 2010-04, Vol.78 (5), p.1084-1104

Antes, Iris

2010

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A Bayesian statistical approach of improving knowledge-based scoring functions for protein-ligand interactions

Journal of computational chemistry, 2014-05, Vol.35 (12), p.932-943

2014

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Data Mining Meets Machine Learning: A Novel ANN‐based Multi‐body Interaction Docking Scoring Function (MBI‐score) Based on Utilizing Frequent Geometric and Chemical Patterns of Interfacial Atoms in Native Protein‐ligand Complexes

Molecular informatics, 2022-08, Vol.41 (8), p.e2100248-n/a

2022

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Comprehensive machine learning boosts structure-based virtual screening for PARP1 inhibitors

Journal of cheminformatics, 2024-04, Vol.16 (1), p.40-40, Article 40

2024

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TS-Chemscore, a Target-Specific Scoring Function, Significantly Improves the Performance of Scoring in Virtual Screening

Chemical biology & drug design, 2015-07, Vol.86 (1), p.1-8

2015

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Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins

Proteins, structure, function, and bioinformatics, 1999-01, Vol.34 (1), p.82-95

1999

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Performance and Its Limits in Rigid Body Protein-Protein Docking

Structure (London), 2020-09, Vol.28 (9), p.1071-1081.e3

2020

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A pharmacophore-based evolutionary approach for screening selective estrogen receptor modulators

Proteins, structure, function, and bioinformatics, 2005-05, Vol.59 (2), p.205-220

2005

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Binding Affinity via Docking: Fact and Fiction

Molecules (Basel, Switzerland), 2018-07, Vol.23 (8), p.1899

2018

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Ab initio protein structure prediction of CASP III targets using ROSETTA

Proteins, structure, function, and bioinformatics, 1999, Vol.37 (S3), p.171-176

1999

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Probabilistic Forecasting

Annual review of statistics and its application, 2014-01, Vol.1 (1), p.125-151

2014

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Automated site preparation in physics-based rescoring of receptor ligand complexes

Proteins, structure, function, and bioinformatics, 2009-10, Vol.77 (1), p.52-61

2009

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Empirical Scoring Functions for Structure-Based Virtual Screening: Applications, Critical Aspects, and Challenges

Frontiers in pharmacology, 2018-09, Vol.9, p.1089-1089

2018

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Improving scoring‐docking‐screening powers of protein–ligand scoring functions using random forest

Journal of computational chemistry, 2017-01, Vol.38 (3), p.169-177

2017

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HIGHER ORDER ELICITABILITY AND OSBAND'S PRINCIPLE

The Annals of statistics, 2016-08, Vol.44 (4), p.1680-1707

2016

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A Structure-Based Drug Discovery Paradigm

International journal of molecular sciences, 2019-06, Vol.20 (11), p.2783

2019

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Comparative binding energy analysis for binding affinity and target selectivity prediction

Proteins, structure, function, and bioinformatics, 2010-01, Vol.78 (1), p.135-153

2010

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Molecular Modeling in Drug Design

2019

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What is the current value of MM/PBSA and MM/GBSA methods in drug discovery?

Expert opinion on drug discovery, 2021-11, Vol.16 (11), p.1233-1237

Tuccinardi, Tiziano

2021

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Beware of the generic machine learning-based scoring functions in structure-based virtual screening

Discovery of novel TRPV1 modulators through machine learning‐based molecular docking and molecular similarity searching

Assessing How Residual Errors of Scoring Functions Correlate to Ligand Structural Features

Machine learning on ligand-residue interaction profiles to significantly improve binding affinity prediction

Multipass membrane protein structure prediction using Rosetta

GalaxyDock BP2 score: a hybrid scoring function for accurate protein–ligand docking

DynaDock: A new molecular dynamics-based algorithm for protein-peptide docking including receptor flexibility

A Bayesian statistical approach of improving knowledge-based scoring functions for protein-ligand interactions

Data Mining Meets Machine Learning: A Novel ANN‐based Multi‐body Interaction Docking Scoring Function (MBI‐score) Based on Utilizing Frequent Geometric and Chemical Patterns of Interfacial Atoms in Native Protein‐ligand Complexes

Comprehensive machine learning boosts structure-based virtual screening for PARP1 inhibitors

TS-Chemscore, a Target-Specific Scoring Function, Significantly Improves the Performance of Scoring in Virtual Screening

Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins

Performance and Its Limits in Rigid Body Protein-Protein Docking

A pharmacophore-based evolutionary approach for screening selective estrogen receptor modulators

Binding Affinity via Docking: Fact and Fiction

Ab initio protein structure prediction of CASP III targets using ROSETTA

Probabilistic Forecasting

Automated site preparation in physics-based rescoring of receptor ligand complexes

Empirical Scoring Functions for Structure-Based Virtual Screening: Applications, Critical Aspects, and Challenges

Improving scoring‐docking‐screening powers of protein–ligand scoring functions using random forest

HIGHER ORDER ELICITABILITY AND OSBAND'S PRINCIPLE

A Structure-Based Drug Discovery Paradigm

Comparative binding energy analysis for binding affinity and target selectivity prediction

Molecular Modeling in Drug Design

What is the current value of MM/PBSA and MM/GBSA methods in drug discovery?

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