Dataset Information

ContraDRG: Automatic Partial Charge Prediction by Machine Learning.

ABSTRACT: In recent years, machine learning techniques have been widely used in biomedical research to predict unseen data based on models trained on experimentally derived data. In the current study, we used machine learning algorithms to emulate computationally complex predictions in a reverse engineering-like manner and developed ContraDRG, a software that can be used to predict partial charges for small molecules based on PRODRG and Automated Topology Builder (ATB) predictions. Both tools generate molecular topology files, including the partial atomic charge, by using different procedures. We show that ContraDRG can accurately predict partial charges in a fraction of the time, because it exploits existing complex models with intensive calculations by using machine learning techniques and thus can also be applied for screening projects with large amounts of molecules. We provide ContraDRG as a web server, which can be used to automatically assign partial charges to incoming user-specified molecules by using our machine learning models. In this study, we compared ContraDRG with PRODRG and ATB in regard of predictivity by statistical methods. ContraDRG allows predicting ATB-derived partial charges with an R² value up to 0.980 and for PRODRG up to 1.00. While ATB requires hours or days for the quantum mechanical accurate calculation and refinements, ContraDRG does its approximation within seconds.

SUBMITTER: Martin R

PROVIDER: S-EPMC6831742 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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ContraDRG: Automatic Partial Charge Prediction by Machine Learning.

Martin Roman R Heider Dominik D

Frontiers in genetics 20191030

In recent years, machine learning techniques have been widely used in biomedical research to predict unseen data based on models trained on experimentally derived data. In the current study, we used machine learning algorithms to emulate computationally complex predictions in a reverse engineering-like manner and developed ContraDRG, a software that can be used to predict partial charges for small molecules based on PRODRG and Automated Topology Builder (ATB) predictions. Both tools generate mol ...[more]

PMID: 31737032

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Project description:BackgroundThe aim of this study was to establish a correlation model between external surface motion and internal diaphragm apex movement using machine learning and to realize online automatic prediction of the diaphragm motion trajectory based on optical surface monitoring.MethodsThe optical body surface parameters and kilovoltage (kV) X-ray fluoroscopic images of 7 liver tumor patients were captured synchronously for 50 seconds. The location of the diaphragm apex was manually delineated by a radiation oncologist and automatically detected with a convolutional network model in fluoroscopic images. The correlation model between the body surface parameters and the diaphragm apex of each patient was developed through linear regression (LR) based on synchronous datasets before radiotherapy. Model 1 (M1) was trained with data from the first 30 seconds of the datasets and tested with data from the following 20 seconds of the datasets in the first fraction to evaluate the intra-fractional prediction accuracy. Model 2 (M2) was trained with data from the first 30 seconds of the datasets in the next fraction. The motion trajectory of the diaphragm apex during the following 20 seconds in the next fraction was predicted with M1 and M2, respectively, to evaluate the inter-fractional prediction accuracy. The prediction errors of the 2 models were compared to analyze whether the correlation model needed to be re-established.ResultsThe average mean absolute error (MAE) and root mean square error (RMSE) using M1 trained with automatic detection location for the first fraction were 3.12±0.80 and 3.82±0.98 mm in the superior-inferior (SI) direction and 1.38±0.24 and 1.74±0.32 mm in the anterior-posterior (AP) direction, respectively. The average MAE and RMSE of M1 versus M2 in the AP direction were 2.63±0.71 versus 1.28±0.48 mm and 3.26±0.90 versus 1.61±0.60 mm, respectively. The average MAE and RMSE of M1 versus M2 in the SI direction were 5.84±1.22 versus 3.37±0.43 mm and 7.22±1.45 versus 4.07±0.54 mm, respectively. The prediction accuracy of M2 was significantly higher than that of M1.ConclusionsThis study shows that it is feasible to use optical body surface information to automatically predict the diaphragm motion trajectory. At the same time, it is necessary to establish a new correlation model for the current fraction before each treatment.

Dataset Information

ContraDRG: Automatic Partial Charge Prediction by Machine Learning.

Publications

ContraDRG: Automatic Partial Charge Prediction by Machine Learning.

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