AIMC Topic: Models, Molecular

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Predictive Modelling in pharmacokinetics: from in-silico simulations to personalized medicine.

Expert opinion on drug metabolism & toxicology Mar 20, 2024
INTRODUCTION: Pharmacokinetic parameters assessment is a critical aspect of drug discovery and development, yet challenges persist due to limited training data. Despite advancements in machine learning and in-silico predictions, scarcity of data hamp...
Humans Models, Biological Drug Design Pharmacokinetics Drug Discovery Pharmacogenetics Drug Development Models, Molecular Pharmaceutical Preparations Computer Simulation Precision Medicine Reproducibility of Results Artificial Intelligence Machine Learning
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PMSPcnn: Predicting protein stability changes upon single point mutations with convolutional neural network.

Structure (London, England : 1993) Mar 19, 2024
Protein missense mutations and resulting protein stability changes are important causes for many human genetic diseases. However, the accurate prediction of stability changes due to mutations remains a challenging problem. To address this problem, we...
Myoglobin DNA Glycosylases Mutation, Missense Point Mutation Humans Neural Networks, Computer Databases, Protein Models, Molecular Protein Stability Tumor Suppressor Protein p53
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PROTACable Is an Integrative Computational Pipeline of 3-D Modeling and Deep Learning To Automate the De Novo Design of PROTACs.

Journal of chemical information and modeling Mar 19, 2024
Proteolysis-targeting chimeras (PROTACs) that engage two biological targets at once are a promising technology in degrading clinically relevant protein targets. Since factors that influence the biological activities of PROTACs are more complex than t...
Drug Design Proteolysis Proteolysis Targeting Chimera Deep Learning Models, Molecular Ubiquitin-Protein Ligases
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Ligand-based pharmacophore modeling and machine learning for the discovery of potent aurora A kinase inhibitory leads of novel chemotypes.

Molecular diversity Mar 6, 2024
Aurora-A (AURKA) is serine/threonine protein kinase involved in the regulation of numerous processes of cell division. Numerous studies have demonstrated strong association between AURKA and cancer. AURKA is overexpressed in many cancers, such as col...
Humans Machine Learning Drug Discovery Protein Kinase Inhibitors Pharmacophore Aurora Kinase A Models, Molecular Ligands Quantitative Structure-Activity Relationship
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Epitope Identification of an mGlu5 Receptor Nanobody Using Physics-Based Molecular Modeling and Deep Learning Techniques.

Journal of chemical information and modeling Feb 29, 2024
The world has witnessed a revolution in therapeutics with the development of biological medicines such as antibodies and antibody fragments, notably nanobodies. These nanobodies possess unique characteristics including high specificity and modulatory...
Single-Domain Antibodies Animals Receptor, Metabotropic Glutamate 5 Rats Molecular Dynamics Simulation Deep Learning Epitope Mapping Models, Molecular Protein Conformation Epitopes
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Investigating the ability of deep learning-based structure prediction to extrapolate and/or enrich the set of antibody CDR canonical forms.

Frontiers in immunology Feb 28, 2024
Deep learning models have been shown to accurately predict protein structure from sequence, allowing researchers to explore protein space from the structural viewpoint. In this paper we explore whether "novel" features, such as distinct loop conforma...
Antibodies Deep Learning Protein Conformation Models, Molecular Complementarity Determining Regions
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Automated model building and protein identification in cryo-EM maps.

Nature Feb 26, 2024
Interpreting electron cryo-microscopy (cryo-EM) maps with atomic models requires high levels of expertise and labour-intensive manual intervention in three-dimensional computer graphics programs. Here we present ModelAngelo, a machine-learning approa...
Computer Graphics Protein Conformation Cryoelectron Microscopy Models, Molecular Neural Networks, Computer Amino Acid Sequence Markov Chains Machine Learning Proteins
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Improved QSAR models for PARP-1 inhibition using data balancing, interpretable machine learning, and matched molecular pair analysis.

Molecular diversity Feb 20, 2024
The poly (ADP-ribose) polymerase-1 (PARP-1) enzyme is an important target in the treatment of breast cancer. Currently, treatment options include the drugs Olaparib, Niraparib, Rucaparib, and Talazoparib; however, these drugs can cause severe side ef...
Quantitative Structure-Activity Relationship Phthalazines Poly(ADP-ribose) Polymerase Inhibitors Humans Poly (ADP-Ribose) Polymerase-1 Machine Learning Algorithms Models, Molecular
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Investigation of bacterial DNA gyrase Inhibitor classification models and structural requirements utilizing multiple machine learning methods.

Molecular diversity Feb 19, 2024
Infections from multidrug-resistant (MDR) bacteria have emerged as a paramount global health concern, and the therapeutic effectiveness of current treatments is swiftly diminishing. An urgent need exists to explore innovative strategies for counterin...
Models, Molecular DNA Gyrase Topoisomerase II Inhibitors Molecular Docking Simulation Bacteria Machine Learning Anti-Bacterial Agents
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Recent Progress of Protein Tertiary Structure Prediction.

Molecules (Basel, Switzerland) Feb 13, 2024
The prediction of three-dimensional (3D) protein structure from amino acid sequences has stood as a significant challenge in computational and structural bioinformatics for decades. Recently, the widespread integration of artificial intelligence (AI)...
Algorithms Computational Biology Proteins Databases, Protein Models, Molecular Protein Conformation Artificial Intelligence Software Protein Folding
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