AIMC Topic: Models, Molecular

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In silico prediction of anti-malarial hit molecules based on machine learning methods.

International journal of computational biology and drug design Apr 13, 2015
Machine learning techniques have been widely used in drug discovery and development in the areas of cheminformatics. Aspartyl aminopeptidase (M18AAP) of Plasmodium falciparum is crucial for survival of malaria parasite. We have created predictive mod...
Models, Statistical Artificial Intelligence Models, Molecular Computer Simulation Antimalarials Drug Discovery
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All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences.

Proceedings of the National Academy of Sciences of the United States of America Apr 9, 2015
Transmembrane β-barrels (TMBs) carry out major functions in substrate transport and protein biogenesis but experimental determination of their 3D structure is challenging. Encouraged by successful de novo 3D structure prediction of globular and α-hel...
Receptors, Cell Surface Protein Structure, Tertiary Sequence Analysis, Protein Models, Molecular Artificial Intelligence Escherichia coli Proteins Escherichia coli Protein Structure, Secondary
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Prediction of overall in vitro microsomal stability of drug candidates based on molecular modeling and support vector machines. Case study of novel arylpiperazines derivatives.

PloS one Mar 31, 2015
Other than efficacy of interaction with the molecular target, metabolic stability is the primary factor responsible for the failure or success of a compound in the drug development pipeline. The ideal drug candidate should be stable enough to reach i...
Half-Life Support Vector Machine Piperazines Microsomes Chromatography, Liquid Tandem Mass Spectrometry Models, Molecular Spectrometry, Mass, Electrospray Ionization
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Improved feature-based prediction of SNPs in human cytochrome P450 enzymes.

Interdisciplinary sciences, computational life sciences Mar 21, 2015
Single nucleotide polymorphisms (SNPs) make up the most common form of mutations in human cytochrome P450 enzymes family, and have the potential to bring with different drug responses or specific diseases in individual patients. Here, based on machin...
Amino Acids Amino Acid Sequence Cytochrome P-450 Enzyme System Area Under Curve Models, Molecular Mutation Base Sequence Codon Artificial Intelligence Phylogeny Polymorphism, Single Nucleotide Computational Biology Support Vector Machine Fuzzy Logic Humans
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Recursive Random Forests Enable Better Predictive Performance and Model Interpretation than Variable Selection by LASSO.

Journal of chemical information and modeling Mar 16, 2015
Variable selection is of crucial significance in QSAR modeling since it increases the model predictive ability and reduces noise. The selection of the right variables is far more complicated than the development of predictive models. In this study, e...
Machine Learning Models, Molecular Quantitative Structure-Activity Relationship Humans Endpoint Determination
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PENG: a neural gas-based approach for pharmacophore elucidation. method design, validation, and virtual screening for novel ligands of LTA4H.

Journal of chemical information and modeling Feb 9, 2015
The pharmacophore concept is commonly employed in virtual screening for hit identification. A pharmacophore is generally defined as the three-dimensional arrangement of the structural and physicochemical features of a compound responsible for its aff...
Thermodynamics Epoxide Hydrolases Reproducibility of Results High-Throughput Screening Assays Protein Binding Enzyme Inhibitors Aminopeptidases Crystallography, X-Ray Models, Molecular Neural Networks, Computer Benchmarking Ligands Algorithms Prospective Studies Humans
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Identifying DNA-binding proteins by combining support vector machine and PSSM distance transformation.

BMC systems biology Feb 6, 2015
BACKGROUND: DNA-binding proteins play a pivotal role in various intra- and extra-cellular activities ranging from DNA replication to gene expression control. Identification of DNA-binding proteins is one of the major challenges in the field of genome...
Support Vector Machine Nucleic Acid Conformation Models, Molecular Molecular Sequence Data Internet Computational Biology DNA-Binding Proteins Sequence Analysis, Protein Amino Acid Sequence Protein Conformation
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Types and effects of protein variations.

Human genetics Jan 24, 2015
Variations in proteins have very large number of diverse effects affecting sequence, structure, stability, interactions, activity, abundance and other properties. Although protein-coding exons cover just over 1 % of the human genome they harbor an di...
Models, Molecular Molecular Dynamics Simulation Amino Acid Sequence Protein Folding Protein Structure, Quaternary Genetic Variation Proteins Humans Gene Ontology Databases, Protein Animals Protein Structure, Secondary Structure-Activity Relationship Protein Processing, Post-Translational
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Beyond current boundaries: Integrating deep learning and AlphaFold for enhanced protein structure prediction from low-resolution cryo-EM maps.

Computational biology and chemistry Dec 1, 2025
Constructing atomic models from cryo-electron microscopy (cryo-EM) maps is a crucial yet intricate task in structural biology. While advancements in deep learning, such as convolutional neural networks (CNNs) and graph neural networks (GNNs), have sp...
Models, Molecular Protein Conformation Cryoelectron Microscopy Neural Networks, Computer Deep Learning Proteins
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Results of the Protein Engineering Tournament: An Open Science Benchmark for Protein Modeling and Design.

Proteins Nov 1, 2025
The grand challenge of protein engineering is the development of computational models to characterize and generate protein sequences for arbitrary functions. Progress is limited by lack of (1) benchmarking opportunities, (2) large protein function da...
Software Algorithms Computational Biology Benchmarking Amino Acid Sequence Protein Conformation Protein Engineering Proteins Databases, Protein Models, Molecular
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