scholarly journals Dataset Augmentation Allows Deep Learning-Based Virtual Screening To Better Generalize To Unseen Target Classes, And Highlight Important Binding Interactions

2020 ◽  
Author(s):  
Jack Scantlebury ◽  
Nathan Brown ◽  
Frank Von Delft ◽  
Charlotte M. Deane
Keyword(s):  
Deep Learning ◽  
Protein Structure ◽  
Virtual Screening ◽  
Ligand Binding ◽  
Training Data ◽  
Learning Methods ◽  
Simple Method ◽  
Physical Interactions ◽  
Account Information ◽  
Protein Models

AbstractCurrent deep learning methods for structure-based virtual screening take the structures of both the protein and the ligand as input but make little or no use of the protein structure when predicting ligand binding. Here we show how a relatively simple method of dataset augmentation forces such deep learning methods to take into account information from the protein. Models trained in this way are more generalisable (make better predictions on protein-ligand complexes from a different distribution to the training data). They also assign more meaningful importance to the protein and ligand atoms involved in binding. Overall, our results show that dataset augmentation can help deep learning based virtual screening to learn physical interactions rather than dataset biases.Graphical TOC Entry

Virtual screening using a conformationally flexible target protein: models for ligand binding to p38α MAPK

2012 ◽  
Vol 26 (4) ◽  
pp. 409-423 ◽  
Author(s):  
Natalie B. Vinh ◽  
Jamie S. Simpson ◽  
Peter J. Scammells ◽  
David K. Chalmers
Keyword(s):  
Virtual Screening ◽  
Ligand Binding ◽  
Target Protein ◽  
P38α Mapk ◽  
Protein Models

scholarly journals Robustness of convolutional neural networks to physiological electrocardiogram noise

2021 ◽  
Vol 379 (2212) ◽  
Author(s):  
J. Venton ◽  
P. M. Harris ◽  
A. Sundar ◽  
N. A. S. Smith ◽  
P. J. Aston
Keyword(s):  
Deep Learning ◽  
Careful Consideration ◽  
Training Data ◽  
Learning Methods ◽  
Ecg Signals ◽  
Open Questions ◽  
Image Transforms ◽  
Challenges And Opportunities ◽  
Electrocardiogram Ecg ◽  
Image Transformations

The electrocardiogram (ECG) is a widespread diagnostic tool in healthcare and supports the diagnosis of cardiovascular disorders. Deep learning methods are a successful and popular technique to detect indications of disorders from an ECG signal. However, there are open questions around the robustness of these methods to various factors, including physiological ECG noise. In this study, we generate clean and noisy versions of an ECG dataset before applying symmetric projection attractor reconstruction (SPAR) and scalogram image transformations. A convolutional neural network is used to classify these image transforms. For the clean ECG dataset, F1 scores for SPAR attractor and scalogram transforms were 0.70 and 0.79, respectively. Scores decreased by less than 0.05 for the noisy ECG datasets. Notably, when the network trained on clean data was used to classify the noisy datasets, performance decreases of up to 0.18 in F1 scores were seen. However, when the network trained on the noisy data was used to classify the clean dataset, the decrease was less than 0.05. We conclude that physiological ECG noise impacts classification using deep learning methods and careful consideration should be given to the inclusion of noisy ECG signals in the training data when developing supervised networks for ECG classification. This article is part of the theme issue ‘Advanced computation in cardiovascular physiology: new challenges and opportunities’.

scholarly journals ROOFN3D: DEEP LEARNING TRAINING DATA FOR 3D BUILDING RECONSTRUCTION

2018 ◽  
Vol XLII-2 ◽  
pp. 1191-1198 ◽  
Author(s):  
A. Wichmann ◽  
A. Agoub ◽  
M. Kada
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Point Cloud ◽  
Geometric Model ◽  
Training Data ◽  
Computer Hardware ◽  
Training Dataset ◽  
3D Point Cloud ◽  
Learning Methods ◽  
Building Reconstruction

Machine learning methods have gained in importance through the latest development of artificial intelligence and computer hardware. Particularly approaches based on deep learning have shown that they are able to provide state-of-the-art results for various tasks. However, the direct application of deep learning methods to improve the results of 3D building reconstruction is often not possible due, for example, to the lack of suitable training data. To address this issue, we present RoofN3D which provides a new 3D point cloud training dataset that can be used to train machine learning models for different tasks in the context of 3D building reconstruction. It can be used, among others, to train semantic segmentation networks or to learn the structure of buildings and the geometric model construction. Further details about RoofN3D and the developed data preparation framework, which enables the automatic derivation of training data, are described in this paper. Furthermore, we provide an overview of other available 3D point cloud training data and approaches from current literature in which solutions for the application of deep learning to unstructured and not gridded 3D point cloud data are presented.

scholarly journals Review of Deep Learning Methods in Robotic Grasp Detection

2018 ◽  
Vol 2 (3) ◽  
pp. 57 ◽  
Author(s):  
Shehan Caldera ◽  
Alexander Rassau ◽  
Douglas Chai
Keyword(s):  
Deep Learning ◽  
Language Processing ◽  
General Purpose ◽  
Training Data ◽  
Learning Approaches ◽  
Automated Driving ◽  
Learning Methods ◽  
Robotic Vision ◽  
Object A ◽  
Robotic Grasp

For robots to attain more general-purpose utility, grasping is a necessary skill to master. Such general-purpose robots may use their perception abilities to visually identify grasps for a given object. A grasp describes how a robotic end-effector can be arranged to securely grab an object and successfully lift it without slippage. Traditionally, grasp detection requires expert human knowledge to analytically form the task-specific algorithm, but this is an arduous and time-consuming approach. During the last five years, deep learning methods have enabled significant advancements in robotic vision, natural language processing, and automated driving applications. The successful results of these methods have driven robotics researchers to explore the use of deep learning methods in task-generalised robotic applications. This paper reviews the current state-of-the-art in regards to the application of deep learning methods to generalised robotic grasping and discusses how each element of the deep learning approach has improved the overall performance of robotic grasp detection. Several of the most promising approaches are evaluated and the most suitable for real-time grasp detection is identified as the one-shot detection method. The availability of suitable volumes of appropriate training data is identified as a major obstacle for effective utilisation of the deep learning approaches, and the use of transfer learning techniques is proposed as a potential mechanism to address this. Finally, current trends in the field and future potential research directions are discussed.

scholarly journals Autonomous molecule generation using reinforcement learning and docking to develop potential novel inhibitors

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Woosung Jeon ◽  
Dongsup Kim
Keyword(s):  
Reinforcement Learning ◽  
Protein Structure ◽  
Virtual Screening ◽  
Computational Method ◽  
Target Protein ◽  
Training Data ◽  
Compound Library ◽  
Lead Compounds ◽  
Large Compound ◽  
Discoidin Domain Receptor 1

AbstractWe developed a computational method named Molecule Optimization by Reinforcement Learning and Docking (MORLD) that automatically generates and optimizes lead compounds by combining reinforcement learning and docking to develop predicted novel inhibitors. This model requires only a target protein structure and directly modifies ligand structures to obtain higher predicted binding affinity for the target protein without any other training data. Using MORLD, we were able to generate potential novel inhibitors against discoidin domain receptor 1 kinase (DDR1) in less than 2 days on a moderate computer. We also demonstrated MORLD’s ability to generate predicted novel agonists for the D4 dopamine receptor (D4DR) from scratch without virtual screening on an ultra large compound library. The free web server is available at http://morld.kaist.ac.kr.

scholarly journals Improved protein structure refinement guided by deep learning based accuracy estimation

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Naozumi Hiranuma ◽  
Hahnbeom Park ◽  
Minkyung Baek ◽  
Ivan Anishchenko ◽  
Justas Dauparas ◽  
...  
Keyword(s):  
Deep Learning ◽  
Protein Structure ◽  
Structure Refinement ◽  
Global Energy ◽  
Accuracy Estimation ◽  
X Ray ◽  
Learning Framework ◽  
Protein Structure Refinement ◽  
Protein Models ◽  
Multiple Stages

AbstractWe develop a deep learning framework (DeepAccNet) that estimates per-residue accuracy and residue-residue distance signed error in protein models and uses these predictions to guide Rosetta protein structure refinement. The network uses 3D convolutions to evaluate local atomic environments followed by 2D convolutions to provide their global contexts and outperforms other methods that similarly predict the accuracy of protein structure models. Overall accuracy predictions for X-ray and cryoEM structures in the PDB correlate with their resolution, and the network should be broadly useful for assessing the accuracy of both predicted structure models and experimentally determined structures and identifying specific regions likely to be in error. Incorporation of the accuracy predictions at multiple stages in the Rosetta refinement protocol considerably increased the accuracy of the resulting protein structure models, illustrating how deep learning can improve search for global energy minima of biomolecules.

scholarly journals Improved protein structure refinement guided by deep learning based accuracy estimation

2020 ◽  
Author(s):  
Naozumi Hiranuma ◽  
Hahnbeom Park ◽  
Minkyung Baek ◽  
Ivan Anishchanka ◽  
Justas Dauparas ◽  
...  
Keyword(s):  
Deep Learning ◽  
Protein Structure ◽  
Structure Refinement ◽  
Global Energy ◽  
Accuracy Estimation ◽  
X Ray ◽  
Learning Framework ◽  
Protein Structure Refinement ◽  
Protein Models ◽  
Multiple Stages

AbstractWe develop a deep learning framework (DeepAccNet) that estimates per-residue accuracy and residue-residue distance signed error in protein models and uses these predictions to guide Rosetta protein structure refinement. The network uses 3D convolutions to evaluate local atomic environments followed by 2D convolutions to provide their global contexts and outperforms other methods that similarly predict the accuracy of protein structure models. Overall accuracy predictions for X-ray and cryoEM structures in the PDB correlate with their resolution, and the network should be broadly useful for assessing the accuracy of both predicted structure models and experimentally determined structures and identifying specific regions likely to be in error. Incorporation of the accuracy predictions at multiple stages in the Rosetta refinement protocol considerably increased the accuracy of the resulting protein structure models, illustrating how deep learning can improve search for global energy minima of biomolecules.

scholarly journals DLAB - Deep learning methods for structure-based virtual screening of antibodies

2021 ◽  
Author(s):  
Constantin Schneider ◽  
Andrew Buchanan ◽  
Bruck Taddese ◽  
Charlotte M. Deane
Keyword(s):  
Deep Learning ◽  
Virtual Screening ◽  
Drug Discovery Process ◽  
Learning Methods ◽  
Drug Candidates ◽  
Specific Antigens ◽  
High Throughput Screens ◽  
Selection Of

AbstractAntibodies are one of the most important classes of pharmaceuticals, with over 80 approved molecules currently in use against a wide variety of diseases. The drug discovery process for antibody therapeutic candidates however is time- and cost-intensive and heavily reliant on in-vivo and in-vitro high throughput screens. Here, we introduce a framework for structure-based deep learning for antibodies (DLAB) which can virtually screen putative binding antibodies against antigen targets of interest. DLAB is built to be able to predict antibody-antigen binding for antigens with no known antibody binders.We demonstrate that DLAB can be used both to improve antibody-antigen docking and structure-based virtual screening of antibody drug candidates. DLAB enables improved pose ranking for antibody docking experiments as well as selection of antibody-antigen pairings for which accurate poses are generated and correctly ranked. DLAB also outperforms baseline methods at identifying binding antibodies against specific antigens in a series of case studies. Our results demonstrate the promise of deep learning methods for structure-based virtual screening of antibodies.

scholarly journals A fully open-source framework for deep learning protein real-valued distances

2020 ◽  
Author(s):  
Badri Adhikari
Keyword(s):  
Deep Learning ◽  
Protein Structure ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Training Data ◽  
Learning Models ◽  
Web Browser ◽  
Fast Development ◽  
Protein Distance ◽  
Distance Prediction

AbstractAs deep learning algorithms drive the progress in protein structure prediction, a lot remains to be studied at this emerging crossway of deep learning and protein structure prediction. Recent findings show that inter-residue distance prediction, a more granular version of the well-known contact prediction problem, is a key to predict accurate models. We believe that deep learning methods that predict these distances are still at infancy. To advance these methods and develop other novel methods, we need a small and representative dataset packaged for fast development and testing. In this work, we introduce Protein Distance Net (PDNET), a dataset derived from the widely used DeepCov dataset and consists of 3456 representative protein chains for training and validation. It is packaged with all the scripts that were used to curate the dataset, generate the input features and distance maps, and scripts with deep learning models to train, validate and test. Deep learning models can also be trained and tested in a web browser using free platforms such as Google Colab. We discuss how this dataset can be used to predict contacts, distance intervals, and real-valued distances (in Å) by designing regression models. All scripts, training data, deep learning code for training, validation, and testing, and Python notebooks are available at https://github.com/ba-lab/pdnet/.

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