AIMC Topic: Drug Design

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Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies.

Journal of chemical theory and computation Jun 4, 2020
Calculating absolute binding free energies is challenging and important. In this paper, we test some recently developed metadynamics-based methods and develop a new combination with a Hamiltonian replica-exchange approach. The methods were tested on ...
Humans Machine Learning Algorithms Ligands Thermodynamics Protein Structure, Tertiary Epoxide Hydrolases Drug Design Protein Binding Molecular Dynamics Simulation
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Deep Learning Based Drug Screening for Novel Coronavirus 2019-nCov.

Interdisciplinary sciences, computational life sciences Jun 1, 2020
A novel coronavirus, called 2019-nCoV, was recently found in Wuhan, Hubei Province of China, and now is spreading across China and other parts of the world. Although there are some drugs to treat 2019-nCoV, there is no proper scientific evidence abou...
Humans Drug Design Deep Learning User-Computer Interface Antiviral Agents Pandemics COVID-19 SARS-CoV-2 Coronavirus 3C Proteases Structural Homology, Protein Betacoronavirus Amino Acid Sequence Pneumonia, Viral Coronavirus Infections Cysteine Endopeptidases Ligands Catalytic Domain Databases, Pharmaceutical Oligopeptides Models, Molecular Databases, Nucleic Acid Viral Nonstructural Proteins Molecular Dynamics Simulation Sequence Alignment Drug Evaluation, Preclinical
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What's new in IBD therapy: An "omics network" approach.

Pharmacological research May 16, 2020
The industrial revolution that began in the late 1800s has resulted in dramatic changes in the environment, human lifestyle, dietary habits, social structure, and so on. Almost certainly because this rapid evolution has outpaced the ability of the bo...
Diffusion of Innovation History, 21st Century History, 20th Century Genomics Systems Biology Gastrointestinal Agents Forecasting Inflammatory Bowel Diseases Animals Drug Discovery Humans Deep Learning Gastroenterology Drug Design
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Binding Affinity Prediction by Pairwise Function Based on Neural Network.

Journal of chemical information and modeling May 11, 2020
We present a new approach to estimate the binding affinity from given three-dimensional poses of protein-ligand complexes. In this scheme, every protein-ligand atom pair makes an additive free-energy contribution. The sum of these pairwise contributi...
Neural Networks, Computer Molecular Docking Simulation Drug Design Protein Binding Ligands
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The SAR Matrix Method and an Artificially Intelligent Variant for the Identification and Structural Organization of Analog Series, SAR Analysis, and Compound Design.

Molecular informatics Apr 20, 2020
The SAR Matrix (SARM) approach was originally conceived for the systematic identification of analog series, their structural organization, and graphical structure-activity relationship (SAR) analysis. For structurally related series, SARMs also produ...
Artificial Intelligence Drug Design Structure-Activity Relationship Pharmaceutical Preparations
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The Synthesizability of Molecules Proposed by Generative Models.

Journal of chemical information and modeling Apr 17, 2020
The discovery of functional molecules is an expensive and time-consuming process, exemplified by the rising costs of small molecule therapeutic discovery. One class of techniques of growing interest for early stage drug discovery is molecular genera...
Drug Design Drug Discovery Neural Networks, Computer Molecular Structure Algorithms
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Revealing cytotoxic substructures in molecules using deep learning.

Journal of computer-aided molecular design Apr 16, 2020
In drug development, late stage toxicity issues of a compound are the main cause of failure in clinical trials. In silico methods are therefore of high importance to guide the early design process to reduce time, costs and animal testing. Technical a...
Humans Neural Networks, Computer Models, Biological Cytotoxins HEK293 Cells Drug Discovery Toxicology Software Deep Learning Small Molecule Libraries Computer-Aided Design Hep G2 Cells Drug Design Cell Survival
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Cov_FB3D: A De Novo Covalent Drug Design Protocol Integrating the BA-SAMP Strategy and Machine-Learning-Based Synthetic Tractability Evaluation.

Journal of chemical information and modeling Apr 9, 2020
drug design actively seeks to use sets of chemical rules for the fast and efficient identification of structurally new chemotypes with the desired set of biological properties. Fragment-based design tools have been successfully applied in the disco...
Enzyme Inhibitors Molecular Conformation Humans Computer Simulation Machine Learning Drug Design Models, Molecular
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The power of deep learning to ligand-based novel drug discovery.

Expert opinion on drug discovery Mar 31, 2020
INTRODUCTION: Deep discriminative and generative neural-network models are becoming an integral part of the modern approach to ligand-based novel drug discovery. The variety of different architectures of neural networks, the methods of their training...
Ligands Humans Neural Networks, Computer Drug Design Algorithms Drug Discovery Deep Learning
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Big data and artificial intelligence discover novel drugs targeting proteins without 3D structure and overcome the undruggable targets.

Stroke and vascular neurology Mar 29, 2020
The discovery of targeted drugs heavily relies on three-dimensional (3D) structures of target proteins. When the 3D structure of a protein target is unknown, it is very difficult to design its corresponding targeted drugs. Although the 3D structures ...
Humans Artificial Intelligence Animals Ligands Big Data Molecular Targeted Therapy Computer-Aided Design Proteins Molecular Structure Databases, Protein Protein Conformation Drug Design Pharmaceutical Preparations Structure-Activity Relationship Drug Discovery Data Mining
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