Dataset Information

Convolutional neural network scoring and minimization in the D3R 2017 community challenge.

ABSTRACT: We assess the ability of our convolutional neural network (CNN)-based scoring functions to perform several common tasks in the domain of drug discovery. These include correctly identifying ligand poses near and far from the true binding mode when given a set of reference receptors and classifying ligands as active or inactive using structural information. We use the CNN to re-score or refine poses generated using a conventional scoring function, Autodock Vina, and compare the performance of each of these methods to using the conventional scoring function alone. Furthermore, we assess several ways of choosing appropriate reference receptors in the context of the D3R 2017 community benchmarking challenge. We find that our CNN scoring function outperforms Vina on most tasks without requiring manual inspection by a knowledgeable operator, but that the pose prediction target chosen for the challenge, Cathepsin S, was particularly challenging for de novo docking. However, the CNN provided best-in-class performance on several virtual screening tasks, underscoring the relevance of deep learning to the field of drug discovery.

SUBMITTER: Sunseri J

PROVIDER: S-EPMC6931043 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

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Convolutional neural network scoring and minimization in the D3R 2017 community challenge.

Sunseri Jocelyn J King Jonathan E JE Francoeur Paul G PG Koes David Ryan DR Koes David Ryan DR

Journal of computer-aided molecular design 20180710 1

We assess the ability of our convolutional neural network (CNN)-based scoring functions to perform several common tasks in the domain of drug discovery. These include correctly identifying ligand poses near and far from the true binding mode when given a set of reference receptors and classifying ligands as active or inactive using structural information. We use the CNN to re-score or refine poses generated using a conventional scoring function, Autodock Vina, and compare the performance of each ...[more]

PMID: 29992528

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Project description:BackgroundThe Psoriasis Area and Severity Index (PASI) score is commonly used in clinical practice and research to monitor disease severity and determine treatment efficacy. Automating the PASI score with deep learning algorithms, like Convolutional Neural Networks (CNNs), could enable objective and efficient PASI scoring.ObjectivesTo assess the performance of image-based automated PASI scoring in anatomical regions by CNNs and compare the performance of CNNs to image-based scoring by physicians.MethodsImaging series were matched to PASI subscores determined in real life by the treating physician. CNNs were trained using standardized imaging series of 576 trunk, 614 arm and 541 leg regions. CNNs were separately trained for each PASI subscore (erythema, desquamation, induration and area) in each anatomical region (trunk, arms and legs). The head region was excluded for anonymity. Additionally, PASI-trained physicians retrospectively determined image-based subscores on the test set images of the trunk. Agreement with the real-life scores was determined with the intraclass correlation coefficient (ICC) and compared between the CNNs and physicians.ResultsIntraclass correlation coefficients between the CNN and real-life scores of the trunk region were 0.616, 0.580, 0.580 and 0.793 for erythema, desquamation, induration and area, respectively, with similar results for the arms and legs region. PASI-trained physicians (N = 5) were in moderate-good agreement (ICCs 0.706-0.793) with each other for image-based PASI scoring of the trunk region. ICCs between the CNN and real-life scores were slightly higher for erythema (0.616 vs. 0.558), induration (0.580 vs. 0.573) and area scoring (0.793 vs. 0.694) than image-based scoring by physicians. Physicians slightly outperformed the CNN on desquamation scoring (0.580 vs. 0.589).ConclusionsConvolutional Neural Networks have the potential to automatically and objectively perform image-based PASI scoring at an anatomical region level. For erythema, desquamation and induration scoring, CNNs performed similar to physicians, while for area scoring CNNs outperformed physicians on image-based PASI scoring.

Dataset Information

Convolutional neural network scoring and minimization in the D3R 2017 community challenge.

Publications

Convolutional neural network scoring and minimization in the D3R 2017 community challenge.

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