scholarly journals DeepBindPoc: a deep learning method to rank ligand binding pockets using molecular vector representation

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8864
Author(s):  
Haiping Zhang ◽  
Konda Mani Saravanan ◽  
Jinzhi Lin ◽  
Linbu Liao ◽  
Justin Tze-Yang Ng ◽  
...  
Keyword(s):  
Deep Learning ◽  
Ligand Binding ◽  
Spatial Information ◽  
Binding Pocket ◽  
Learning Method ◽  
Accurate Identification ◽  
Data Set ◽  
Structure Based Drug Design ◽  
Binding Pockets ◽  
High Level

Accurate identification of ligand-binding pockets in a protein is important for structure-based drug design. In recent years, several deep learning models were developed to learn important physical–chemical and spatial information to predict ligand-binding pockets in a protein. However, ranking the native ligand binding pockets from a pool of predicted pockets is still a hard task for computational molecular biologists using a single web-based tool. Hence, we believe, by using closer to real application data set as training and by providing ligand information, an enhanced model to identify accurate pockets can be obtained. In this article, we propose a new deep learning method called DeepBindPoc for identifying and ranking ligand-binding pockets in proteins. The model is built by using information about the binding pocket and associated ligand. We take advantage of the mol2vec tool to represent both the given ligand and pocket as vectors to construct a densely fully connected layer model. During the training, important features for pocket-ligand binding are automatically extracted and high-level information is preserved appropriately. DeepBindPoc demonstrated a strong complementary advantage for the detection of native-like pockets when combined with traditional popular methods, such as fpocket and P2Rank. The proposed method is extensively tested and validated with standard procedures on multiple datasets, including a dataset with G-protein Coupled receptors. The systematic testing and validation of our method suggest that DeepBindPoc is a valuable tool to rank near-native pockets for theoretically modeled protein with unknown experimental active site but have known ligand. The DeepBindPoc model described in this article is available at GitHub (https://github.com/haiping1010/DeepBindPoc) and the webserver is available at (http://cbblab.siat.ac.cn/DeepBindPoc/index.php).

scholarly journals A Novel Method of Hyperspectral Data Classification Based on Transfer Learning and Deep Belief Network

2019 ◽  
Vol 9 (7) ◽  
pp. 1379 ◽  
Author(s):  
Ke Li ◽  
Mingju Wang ◽  
Yixin Liu ◽  
Nan Yu ◽  
Wei Lan
Keyword(s):  
Deep Learning ◽  
Transfer Learning ◽  
Spatial Information ◽  
Hyperspectral Data ◽  
Deep Belief Network ◽  
Learning Method ◽  
Target Domain ◽  
Data Set ◽  
Belief Network ◽  
Target Data

The classification of hyperspectral data using deep learning methods can obtain better results than the previous shallow classifiers, but deep learning algorithms have some limitations. These algorithms require a large amount of data to train the network, while also needing a certain amount of labeled data to fine-tune the network. In this paper, we propose a new hyperspectral data processing method based on transfer learning and the deep learning method. First, we use a hyperspectral data set that is similar to the target data set to pre-train the deep learning network. Then, we use the transfer learning method to find the common features of the source domain data and target domain data. Second, we propose a model structure that combines the deep transfer learning model to utilize a combination of spatial information and spectral information. Using transfer learning, we can obtain the spectral features. Then, we obtain several principal components of the target data. These will be regarded as the spatial features of the target domain data, and we use the joint features for the classifier. The data are obtained from a hyperspectral public database. Using the same amount of data, our method based on transfer learning and deep belief network obtains better classification accuracy in a shorter amount of time.

scholarly journals DEELIG: A Deep Learning Approach to Predict Protein-Ligand Binding Affinity

2021 ◽  
Vol 15 ◽  
pp. 117793222110303
Author(s):  
Asad Ahmed ◽  
Bhavika Mam ◽  
Ramanathan Sowdhamini
Keyword(s):  
Deep Learning ◽  
Ligand Binding ◽  
Binding Affinity ◽  
Chemical Space ◽  
Biological Significance ◽  
Protein Crystal ◽  
Ligand Docking ◽  
Complex Data ◽  
Binding Prediction ◽  
Data Set

Protein-ligand binding prediction has extensive biological significance. Binding affinity helps in understanding the degree of protein-ligand interactions and is a useful measure in drug design. Protein-ligand docking using virtual screening and molecular dynamic simulations are required to predict the binding affinity of a ligand to its cognate receptor. Performing such analyses to cover the entire chemical space of small molecules requires intense computational power. Recent developments using deep learning have enabled us to make sense of massive amounts of complex data sets where the ability of the model to “learn” intrinsic patterns in a complex plane of data is the strength of the approach. Here, we have incorporated convolutional neural networks to find spatial relationships among data to help us predict affinity of binding of proteins in whole superfamilies toward a diverse set of ligands without the need of a docked pose or complex as user input. The models were trained and validated using a stringent methodology for feature extraction. Our model performs better in comparison to some existing methods used widely and is suitable for predictions on high-resolution protein crystal (⩽2.5 Å) and nonpeptide ligand as individual inputs. Our approach to network construction and training on protein-ligand data set prepared in-house has yielded significant insights. We have also tested DEELIG on few COVID-19 main protease-inhibitor complexes relevant to the current public health scenario. DEELIG-based predictions can be incorporated in existing databases including RSCB PDB, PDBMoad, and PDBbind in filling missing binding affinity data for protein-ligand complexes.

scholarly journals Simulation and Recognition of Concrete Lining Infiltration Degree via an Indoor Experiment

Geofluids ◽  
2020 ◽  
Vol 2020 ◽  
pp. 1-11
Author(s):  
Dongsheng Wang ◽  
Jun Feng ◽  
Xinpeng Zhao ◽  
Yeping Bai ◽  
Yujie Wang ◽  
...  
Keyword(s):  
Deep Learning ◽  
Cement Mortar ◽  
Recognition Accuracy ◽  
Image Data ◽  
Concrete Lining ◽  
Learning Method ◽  
Recognition Method ◽  
Data Set ◽  
Recognition Model ◽  
High Recognition Accuracy

It is difficult to form a method for recognizing the degree of infiltration of a tunnel lining. To solve this problem, we propose a recognition method by using a deep convolutional neural network. We carry out laboratory tests, prepare cement mortar specimens with different saturation levels, simulate different degrees of infiltration of tunnel concrete linings, and establish an infrared thermal image data set with different degrees of infiltration. Then, based on a deep learning method, the data set is trained using the Faster R-CNN+ResNet101 network, and a recognition model is established. The experiments show that the recognition model established by the deep learning method can be used to select cement mortar specimens with different degrees of infiltration by using an accurately minimized rectangular outer frame. This model shows that the classification recognition model for tunnel concrete lining infiltration established by the indoor experimental method has high recognition accuracy.

scholarly journals BionoiNet: ligand-binding site classification with off-the-shelf deep neural network

2020 ◽  
Vol 36 (10) ◽  
pp. 3077-3083
Author(s):  
Wentao Shi ◽  
Jeffrey M Lemoine ◽  
Abd-El-Monsif A Shawky ◽  
Manali Singha ◽  
Limeng Pu ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Ligand Binding ◽  
Binding Sites ◽  
Protein Structures ◽  
Supplementary Information ◽  
Heme Binding ◽  
Unseen Data ◽  
Ligand Binding Sites ◽  
Binding Pockets

Abstract Motivation Fast and accurate classification of ligand-binding sites in proteins with respect to the class of binding molecules is invaluable not only to the automatic functional annotation of large datasets of protein structures but also to projects in protein evolution, protein engineering and drug development. Deep learning techniques, which have already been successfully applied to address challenging problems across various fields, are inherently suitable to classify ligand-binding pockets. Our goal is to demonstrate that off-the-shelf deep learning models can be employed with minimum development effort to recognize nucleotide- and heme-binding sites with a comparable accuracy to highly specialized, voxel-based methods. Results We developed BionoiNet, a new deep learning-based framework implementing a popular ResNet model for image classification. BionoiNet first transforms the molecular structures of ligand-binding sites to 2D Voronoi diagrams, which are then used as the input to a pretrained convolutional neural network classifier. The ResNet model generalizes well to unseen data achieving the accuracy of 85.6% for nucleotide- and 91.3% for heme-binding pockets. BionoiNet also computes significance scores of pocket atoms, called BionoiScores, to provide meaningful insights into their interactions with ligand molecules. BionoiNet is a lightweight alternative to computationally expensive 3D architectures. Availability and implementation BionoiNet is implemented in Python with the source code freely available at: https://github.com/CSBG-LSU/BionoiNet. Supplementary information Supplementary data are available at Bioinformatics online.

Chemical parameters influencing fine-tuning in the binding of macrolide antibiotics to the ribosomal tunnel

2007 ◽  
Vol 79 (6) ◽  
pp. 955-968 ◽  
Author(s):  
Erez Pyetan ◽  
David Baram ◽  
Tamar Auerbach-Nevo ◽  
Ada Yonath
Keyword(s):  
Deinococcus Radiodurans ◽  
Bacterial Species ◽  
Ribosomal Subunit ◽  
Binding Pocket ◽  
Fine Tuning ◽  
23S Rrna ◽  
Structure Based Drug Design ◽  
Altered Level ◽  
Ribosomal Tunnel ◽  
Binding Pockets

In comparison to existing structural, biochemical, and therapeutical data, the crystal structures of large ribosomal subunit from the eubacterial pathogen model Deinococcus radiodurans in complex with the 14-membered macrolides erythromycylamine, RU69874, and the 16-membered macrolide josamycin, highlighted the similarities and differences in macrolides binding to the ribosomal tunnel. The three compounds occupy the macrolide binding pocket with their desosamine or mycaminose aminosugar, the C4-C7 edge of the macrolactone ring and the cladinose sugar sharing similar positions and orientations, although the latter, known to be unnecessary for antibiotic activity, displays fewer contacts. The macrolactone ring displays altogether few contacts with the ribosome and can, therefore, tilt in order to optimize its interaction with the 23S rRNA. In addition to their contacts with nucleotides of domain V of the 23S RNA, erythromycylamine and RU69874 interact with domain II nucleotide U790, and RU69874 also reaches van der Waals distance from A752, in a fashion similar to that observed for the ketolides telithromycin and cethromycin. The variability in the sequences and consequently the diversity of the conformations of macrolide binding pockets in various bacterial species can explain the drug's altered level of effectiveness on different organisms and is thus an important factor in structure-based drug design.

scholarly journals Deep Learning to Detect Skin Cancer using Google Colab

2019 ◽  
Vol 8 (6) ◽  
pp. 2176-2183 ◽  
Keyword(s):  
Artificial Intelligence ◽  
Machine Learning ◽  
Deep Learning ◽  
Skin Cancer ◽  
Domain Knowledge ◽  
Error Rates ◽  
Data Set ◽  
Training Models ◽  
Learning Machine ◽  
High Level

Different mathematical models, Artificial Intelligence approach and Past recorded data set is combined to formulate Machine Learning. Machine Learning uses different learning algorithms for different types of data and has been classified into three types. The advantage of this learning is that it uses Artificial Neural Network and based on the error rates, it adjusts the weights to improve itself in further epochs. But, Machine Learning works well only when the features are defined accurately. Deciding which feature to select needs good domain knowledge which makes Machine Learning developer dependable. The lack of domain knowledge affects the performance. This dependency inspired the invention of Deep Learning. Deep Learning can detect features through self-training models and is able to give better results compared to using Artificial Intelligence or Machine Learning. It uses different functions like ReLU, Gradient Descend and Optimizers, which makes it the best thing available so far. To efficiently apply such optimizers, one should have the knowledge of mathematical computations and convolutions running behind the layers. It also uses different pooling layers to get the features. But these Modern Approaches need high level of computation which requires CPU and GPUs. In case, if, such high computational power, if hardware is not available then one can use Google Colaboratory framework. The Deep Learning Approach is proven to improve the skin cancer detection as demonstrated in this paper. The paper also aims to provide the circumstantial knowledge to the reader of various practices mentioned above.

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