ProDCoNN: Protein design using a convolutional neural network.
Ontology highlight
ABSTRACT:
SUBMITTER: Zhang Y
PROVIDER: S-EPMC8204568 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The analysis and comparison of protein-binding sites aid various applications in the drug discovery process, e.g., hit finding, drug repurposing, and polypharmacology. Classification of binding sites has been a hot topic for the past 30 years, and many different methods have been published. The rapid development of machine learning computational algorithms, coupled with the large volume of publicly available protein-ligand 3D structures, makes it possible to apply deep learning techniques in binding site comparison. Our method uses a cutting-edge spherical convolutional neural network based on the DeepSphere architecture to learn global representations of protein-binding sites. The model was trained on TOUGH-C1 and TOUGH-M1 data and validated with the ProSPECCTs datasets. Our results show that our model can (1) perform well in protein-binding site similarity and classification tasks and (2) learn and separate the physicochemical properties of binding sites. Lastly, we tested the model on a set of kinases, where the results show that it is able to cluster the different kinase subfamilies effectively. This example demonstrates the method's promise for lead hopping within or outside a protein target, directly based on binding site information.
| S-EPMC9709917 | biostudies-literature
Project description:Interventions: None
Primary outcome(s): The primary outcome of the study is the accuracy of the CAD-CNN system for predicting histology of diminutive colorectal polyps (1-5mm) compared with the accuracy of the prediction of the endoscopist. Both the CAD-CNN system and the endoscopist will use NBI for their predictions.
Accuracy is defined as the percentage of correctly predicted optical diagnoses of the CAD-CNN system and/or endoscopist compared to the gold standard pathology. For the calculation of the accuracy, adenomas and SSLs will be dichotomised as neoplastic polyps, while HPs and other non-neoplastic histology are considered non-neoplastic.
Study Design: N/A: single arm study, Open (masking not used), N/A , unknown, Other
| 2443187 | ecrin-mdr-crc
Project description:Protein-ligand scoring is an important step in a structure-based drug design pipeline. Selecting a correct binding pose and predicting the binding affinity of a protein-ligand complex enables effective virtual screening. Machine learning techniques can make use of the increasing amounts of structural data that are becoming publicly available. Convolutional neural network (CNN) scoring functions in particular have shown promise in pose selection and affinity prediction for protein-ligand complexes. Neural networks are known for being difficult to interpret. Understanding the decisions of a particular network can help tune parameters and training data to maximize performance. Visualization of neural networks helps decompose complex scoring functions into pictures that are more easily parsed by humans. Here we present three methods for visualizing how individual protein-ligand complexes are interpreted by 3D convolutional neural networks. We also present a visualization of the convolutional filters and their weights. We describe how the intuition provided by these visualizations aids in network design.
| S-EPMC6343664 | biostudies-literature
Project description:Protein-protein interaction (PPI) sites play a key role in the formation of protein complexes, which is the basis of a variety of biological processes. Experimental methods to solve PPI sites are expensive and time-consuming, which has led to the development of different kinds of prediction algorithms. We propose a convolutional neural network for PPI site prediction and use residue binding propensity to improve the positive samples. Our method obtains a remarkable result of the area under the curve (AUC) = 0.912 on the improved data set. In addition, it yields much better results on samples with high binding propensity than on randomly selected samples. This suggests that there are considerable false-positive PPI sites in the positive samples defined by the distance between residue atoms.
| S-EPMC7013409 | biostudies-literature
Project description:Recently, social touch gesture recognition has been considered an important topic for touch modality, which can lead to highly efficient and realistic human-robot interaction. In this paper, a deep convolutional neural network is selected to implement a social touch recognition system for raw input samples (sensor data) only. The touch gesture recognition is performed using a dataset previously measured with numerous subjects that perform varying social gestures. This dataset is dubbed as the corpus of social touch, where touch was performed on a mannequin arm. A leave-one-subject-out cross-validation method is used to evaluate system performance. The proposed method can recognize gestures in nearly real time after acquiring a minimum number of frames (the average range of frame length was from 0.2% to 4.19% from the original frame lengths) with a classification accuracy of 63.7%. The achieved classification accuracy is competitive in terms of the performance of existing algorithms. Furthermore, the proposed system outperforms other classification algorithms in terms of classification ratio and touch recognition time without data preprocessing for the same dataset.
| S-EPMC6197001 | biostudies-literature
Project description:With the introduction of various advanced deep learning algorithms, initiatives for image classification systems have transitioned over from traditional machine learning algorithms (e.g., SVM) to Convolutional Neural Networks (CNNs) using deep learning software tools. A prerequisite in applying CNN to real world applications is a system that collects meaningful and useful data. For such purposes, Wireless Image Sensor Networks (WISNs), that are capable of monitoring natural environment phenomena using tiny and low-power cameras on resource-limited embedded devices, can be considered as an effective means of data collection. However, with limited battery resources, sending high-resolution raw images to the backend server is a burdensome task that has direct impact on network lifetime. To address this problem, we propose an energy-efficient pre- and post- processing mechanism using image resizing and color quantization that can significantly reduce the amount of data transferred while maintaining the classification accuracy in the CNN at the backend server. We show that, if well designed, an image in its highly compressed form can be well-classified with a CNN model trained in advance using adequately compressed data. Our evaluation using a real image dataset shows that an embedded device can reduce the amount of transmitted data by ∼71% while maintaining a classification accuracy of ∼98%. Under the same conditions, this process naturally reduces energy consumption by ∼71% compared to a WISN that sends the original uncompressed images.
| S-EPMC5940226 | biostudies-literature
Project description:The automatic detection of atrial fibrillation (AF) is crucial for its association with the risk of embolic stroke. Most of the existing AF detection methods usually convert 1D time-series electrocardiogram (ECG) signal into 2D spectrogram to train a complex AF detection system, which results in heavy training computation and high implementation cost. This paper proposes an AF detection method based on an end-to-end 1D convolutional neural network (CNN) architecture to raise the detection accuracy and reduce network complexity. By investigating the impact of major components of a convolutional block on detection accuracy and using grid search to obtain optimal hyperparameters of the CNN, we develop a simple, yet effective 1D CNN. Since the dataset provided by PhysioNet Challenge 2017 contains ECG recordings with different lengths, we also propose a length normalization algorithm to generate equal-length records to meet the requirement of CNN. Experimental results and analysis indicate that our method of 1D CNN achieves an average F1 score of 78.2%, which has better detection accuracy with lower network complexity, as compared with the existing deep learning-based methods.
| S-EPMC7180882 | biostudies-literature
Project description:BackgroundUltrasound (US) is widely used in the clinical diagnosis of thyroid nodules. Artificial intelligence-powered US is becoming an important issue in the research community. This study aimed to develop an improved deep learning model-based algorithm to classify benign and malignant thyroid nodules (TNs) using thyroid US images.MethodsIn total, 592 patients with 600 TNs were included in the internal training, validation, and testing data set; 187 patients with 200 TNs were recruited for the external test data set. We developed a Visual Geometry Group (VGG)-16T model, based on the VGG-16 architecture, but with additional batch normalization (BN) and dropout layers in addition to the fully connected layers. We conducted a 10-fold cross-validation to analyze the performance of the VGG-16T model using a data set of gray-scale US images from 5 different brands of US machines.ResultsFor the internal data set, the VGG-16T model had 87.43% sensitivity, 85.43% specificity, and 86.43% accuracy. For the external data set, the VGG-16T model achieved an area under the curve (AUC) of 0.829 [95% confidence interval (CI): 0.770-0.879], a radiologist with 15 years' working experience achieved an AUC of 0.705 (95% CI: 0.659-0.801), a radiologist with 10 years' experience achieved an AUC of 0.725 (95% CI: 0.653-0.797), and a radiologist with 5 years' experience achieved an AUC of 0.660 (95% CI: 0.584-0.736).ConclusionsThe VGG-16T model had high specificity, sensitivity, and accuracy in differentiating between malignant and benign TNs. Its diagnostic performance was superior to that of experienced radiologists. Thus, the proposed improved deep-learning model can assist radiologists to diagnose thyroid cancer.
| S-EPMC8576712 | biostudies-literature
Project description:A deep machine-learning technique based on a convolutional neural network (CNN) is introduced. It has been used for the classification of powder X-ray diffraction (XRD) patterns in terms of crystal system, extinction group and space group. About 150 000 powder XRD patterns were collected and used as input for the CNN with no handcrafted engineering involved, and thereby an appropriate CNN architecture was obtained that allowed determination of the crystal system, extinction group and space group. In sharp contrast with the traditional use of powder XRD pattern analysis, the CNN never treats powder XRD patterns as a deconvoluted and discrete peak position or as intensity data, but instead the XRD patterns are regarded as nothing but a pattern similar to a picture. The CNN interprets features that humans cannot recognize in a powder XRD pattern. As a result, accuracy levels of 81.14, 83.83 and 94.99% were achieved for the space-group, extinction-group and crystal-system classifications, respectively. The well trained CNN was then used for symmetry identification of unknown novel inorganic compounds.
| S-EPMC5571811 | biostudies-literature
Project description:MotivationConvolutional neural networks (CNN) have outperformed conventional methods in modeling the sequence specificity of DNA-protein binding. Yet inappropriate CNN architectures can yield poorer performance than simpler models. Thus an in-depth understanding of how to match CNN architecture to a given task is needed to fully harness the power of CNNs for computational biology applications.ResultsWe present a systematic exploration of CNN architectures for predicting DNA sequence binding using a large compendium of transcription factor datasets. We identify the best-performing architectures by varying CNN width, depth and pooling designs. We find that adding convolutional kernels to a network is important for motif-based tasks. We show the benefits of CNNs in learning rich higher-order sequence features, such as secondary motifs and local sequence context, by comparing network performance on multiple modeling tasks ranging in difficulty. We also demonstrate how careful construction of sequence benchmark datasets, using approaches that control potentially confounding effects like positional or motif strength bias, is critical in making fair comparisons between competing methods. We explore how to establish the sufficiency of training data for these learning tasks, and we have created a flexible cloud-based framework that permits the rapid exploration of alternative neural network architectures for problems in computational biology.Availability and implementationAll the models analyzed are available at http://cnn.csail.mit.eduContactgifford@mit.eduSupplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC4908339 | biostudies-literature