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Binding Sites

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Prediction of Protein-Protein Interaction Sites Using Convolutional Neural Network and Improved Data Sets.

International journal of molecular sciences Jan 11, 2020
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 dev...
Datasets as Topic Binding Sites Protein Interaction Mapping Humans Animals Neural Networks, Computer Protein Binding Reproducibility of Results
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Deep neural network affinity model for BACE inhibitors in D3R Grand Challenge 4.

Journal of computer-aided molecular design Jan 8, 2020
Drug Design Data Resource (D3R) Grand Challenge 4 (GC4) offered a unique opportunity for designing and testing novel methodology for accurate docking and affinity prediction of ligands in an open and blinded manner. We participated in the beta-secret...
Humans Neural Networks, Computer Molecular Docking Simulation Drug Design Macrocyclic Compounds Protein Binding Binding Sites Ligands Amyloid Precursor Protein Secretases Enzyme Inhibitors Aspartic Acid Endopeptidases
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Representation learning of genomic sequence motifs with convolutional neural networks.

PLoS computational biology Dec 19, 2019
Although convolutional neural networks (CNNs) have been applied to a variety of computational genomics problems, there remains a large gap in our understanding of how they build representations of regulatory genomic sequences. Here we perform systema...
Humans Neural Networks, Computer Computer Simulation Deep Learning Binding Sites Amino Acid Motifs Databases, Genetic DNA Genome, Human Genomics Computational Biology Transcription Factors
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Latest trends in structure based drug design with protein targets.

Advances in protein chemistry and structural biology Dec 18, 2019
Structure based drug designing is an important endeavor in the field of structural bioinformatics. Previously the entire process was dependent on the wet-lab experiments to build libraries of ligand molecules. And the molecules used to be tested to d...
Proteins Structure-Activity Relationship Molecular Dynamics Simulation Ligands Protein Binding Computational Biology Neuroprotective Agents Binding Sites Thermodynamics Drugs, Investigational Humans Machine Learning Anti-Bacterial Agents Antineoplastic Agents Anti-HIV Agents Molecular Docking Simulation Drug Design
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MathDL: mathematical deep learning for D3R Grand Challenge 4.

Journal of computer-aided molecular design Nov 16, 2019
We present the performances of our mathematical deep learning (MathDL) models for D3R Grand Challenge 4 (GC4). This challenge involves pose prediction, affinity ranking, and free energy estimation for beta secretase 1 (BACE) as well as affinity ranki...
Aspartic Acid Endopeptidases Binding Sites Thermodynamics Small Molecule Libraries Cathepsins Protein Binding Ligands Molecular Docking Simulation Amyloid Precursor Protein Secretases Drug Design Deep Learning Humans
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Exploring fragment-based target-specific ranking protocol with machine learning on cathepsin S.

Journal of computer-aided molecular design Nov 15, 2019
Cathepsin S (CatS), a member of cysteine cathepsin proteases, has been well studied due to its significant role in many pathological processes, including arthritis, cancer and cardiovascular diseases. CatS inhibitors have been included in D3R-GC3 for...
Humans Machine Learning Binding Sites Thermodynamics Cathepsins Databases, Protein Ligands Crystallography, X-Ray Protein Conformation Molecular Docking Simulation Computer-Aided Design Protein Binding
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Identifying Cancer-Specific circRNA-RBP Binding Sites Based on Deep Learning.

Molecules (Basel, Switzerland) Nov 7, 2019
Circular RNAs (circRNAs) are extensively expressed in cells and tissues, and play crucial roles in human diseases and biological processes. Recent studies have reported that circRNAs could function as RNA binding protein (RBP) sponges, meanwhile RBPs...
Sequence Analysis, Protein RNA, Neoplasm RNA, Circular Databases, Protein Neoplasm Proteins Binding Sites Deep Learning RNA-Binding Proteins Humans Neoplasms
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Recognizing five molecular ligand-binding sites with similar chemical structure.

Journal of computational chemistry Oct 23, 2019
Accurate identification of ligand-binding sites and discovering the protein-ligand interaction mechanism are important for understanding proteins' functions and designing new drugs. Meanwhile, accurate computational prediction and mechanism research ...
Guanosine Diphosphate Support Vector Machine NAD Ligands Guanosine Triphosphate Binding Sites Proteins Adenosine Diphosphate Adenosine Triphosphate
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Graph Convolutional Neural Networks for Predicting Drug-Target Interactions.

Journal of chemical information and modeling Oct 16, 2019
Accurate determination of target-ligand interactions is crucial in the drug discovery process. In this paper, we propose a graph-convolutional (Graph-CNN) framework for predicting protein-ligand interactions. First, we built an unsupervised graph-aut...
Neural Networks, Computer Drug Discovery Protein Binding Databases, Chemical Binding Sites Drug Development Protein Conformation Proteins Ligands
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econvRBP: Improved ensemble convolutional neural networks for RNA binding protein prediction directly from sequence.

Methods (San Diego, Calif.) Sep 9, 2019
RNA binding proteins (RBPs) determine RNA process from synthesis to decay, which play a key role in RNA transport, translation and degradation. Therefore, exploring RBPs' function from the amino acid sequence using computational methods has become on...
Binding Sites Amino Acid Sequence Deep Learning RNA Computational Biology Sequence Analysis, Protein Datasets as Topic RNA-Binding Proteins
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