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   Articles with "scoring function" as a keyword



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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

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recommendations! Published in 2022 at "Molecular Informatics"

DOI: 10.1002/minf.202100248

Abstract: Accurate prediction of binding poses is crucial to structure‐based drug design. We employ two powerful artificial intelligence (AI) approaches, data‐mining and machine‐learning, to design artificial neural network (ANN) based pose‐scoring function. It is a simple… read more here.

Keywords: function; scoring function; machine learning; mbi score ... See more keywords
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GB‐score: Minimally designed machine learning scoring function based on distance‐weighted interatomic contact features

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recommendations! Published in 2022 at "Molecular Informatics"

DOI: 10.1002/minf.202200135

Abstract: In recent years, thanks to advances in computer hardware and dataset availability, data‐driven approaches (like machine learning) have become one of the essential parts of the drug design framework to accelerate drug discovery procedures. Constructing… read more here.

Keywords: function; machine; scoring function; machine learning ... See more keywords
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GalaxyDock BP2 score: a hybrid scoring function for accurate protein–ligand docking

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recommendations! Published in 2017 at "Journal of Computer-Aided Molecular Design"

DOI: 10.1007/s10822-017-0030-9

Abstract: Protein–ligand docking is a useful tool for providing atomic-level understanding of protein functions in nature and design principles for artificial ligands or proteins with desired properties. The ability to identify the true binding pose of… read more here.

Keywords: protein; scoring function; galaxydock bp2; score ... See more keywords
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Forging the Basis for Developing Protein-Ligand Interaction Scoring Functions.

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recommendations! Published in 2017 at "Accounts of chemical research"

DOI: 10.1021/acs.accounts.6b00491

Abstract: In structure-based drug design, scoring functions are widely used for fast evaluation of protein-ligand interactions. They are often applied in combination with molecular docking and de novo design methods. Since the early 1990s, a whole… read more here.

Keywords: scoring function; scoring functions; protein ligand; ligand interaction ... See more keywords
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Improving Protein-Peptide Docking Results via Pose-Clustering and Rescoring with a Combined Knowledge-Based and MM-GBSA Scoring Function

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recommendations! Published in 2020 at "Journal of chemical information and modeling"

DOI: 10.1021/acs.jcim.0c00058

Abstract: Protein-peptide docking, which predicts the complex structure between a protein and a peptide, is a valuable computational tool in peptide therapeutics development and mechanistic investigation of peptides involved cellular processes. Although current peptide docking approaches… read more here.

Keywords: knowledge based; scoring function; post docking; peptide docking ... See more keywords
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Development of a New Scoring Function for Virtual Screening: APBScore

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recommendations! Published in 2020 at "Journal of chemical information and modeling"

DOI: 10.1021/acs.jcim.0c00474

Abstract: In this study, we developed a new physical-based scoring function, Atom Pair-Based Scoring function (APBScore), which includes pairwise van der Waals (VDW), electrostatic interaction, and hydrogen bond energies between the receptor and ligand. Despite the… read more here.

Keywords: apbscore; scoring functions; development new; scoring function ... See more keywords
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AA-Score: a New Scoring Function Based on Amino Acid-Specific Interaction for Molecular Docking.

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recommendations! Published in 2022 at "Journal of chemical information and modeling"

DOI: 10.1021/acs.jcim.1c01537

Abstract: The protein-ligand scoring function plays an important role in computer-aided drug discovery and is heavily used in virtual screening and lead optimization. In this study, we developed a new empirical protein-ligand scoring function with amino… read more here.

Keywords: interaction; scoring function; amino acid; function ... See more keywords
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A Small Step Toward Generalizability: Training a Machine Learning Scoring Function for Structure-Based Virtual Screening

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recommendations! Published in 2023 at "Journal of Chemical Information and Modeling"

DOI: 10.1021/acs.jcim.3c00322

Abstract: Over the past few years, many machine learning-based scoring functions for predicting the binding of small molecules to proteins have been developed. Their objective is to approximate the distribution which takes two molecules as input… read more here.

Keywords: function; scoring functions; scoring function; machine learning ... See more keywords
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Protein-Ligand Scoring with Convolutional Neural Networks

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recommendations! Published in 2017 at "Journal of chemical information and modeling"

DOI: 10.1021/acs.jcim.6b00740

Abstract: Computational approaches to drug discovery can reduce the time and cost associated with experimental assays and enable the screening of novel chemotypes. Structure-based drug design methods rely on scoring functions to rank and predict binding… read more here.

Keywords: scoring functions; scoring function; ligand scoring; convolutional neural ... See more keywords
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Converging a Knowledge-Based Scoring Function: DrugScore2018

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recommendations! Published in 2019 at "Journal of chemical information and modeling"

DOI: 10.1021/acs.jcim.8b00582

Abstract: We present DrugScore2018, a new version of the knowledge-based scoring function DrugScore, which builds upon the same formalism used to derive DrugScore but exploits a training data set of nearly 40 000 X-ray complex structures, a… read more here.

Keywords: knowledge based; based scoring; scoring function; drugscore2018 ... See more keywords
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Improving protein-ligand docking and screening accuracies by incorporating a scoring function correction term.

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recommendations! Published in 2022 at "Briefings in bioinformatics"

DOI: 10.1093/bib/bbac051

Abstract: Scoring functions are important components in molecular docking for structure-based drug discovery. Traditional scoring functions, generally empirical- or force field-based, are robust and have proven to be useful for identifying hits and lead optimizations. Although… read more here.

Keywords: docking screening; function; protein ligand; scoring function ... See more keywords