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Models, Molecular

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XGBoost odor prediction model: finding the structure-odor relationship of odorant molecules using the extreme gradient boosting algorithm.

Journal of biomolecular structure & dynamics Sep 18, 2023
Determining the structure-odor relationship has always been a very challenging task. The main challenge in investigating the correlation between the molecular structure and its associated odor is the ambiguous and obscure nature of verbally defined o...
Algorithms Models, Molecular Machine Learning Smell Quantitative Structure-Activity Relationship Molecular Structure Odorants
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Integrating deep learning, threading alignments, and a multi-MSA strategy for high-quality protein monomer and complex structure prediction in CASP15.

Proteins Aug 31, 2023
We report the results of the "UM-TBM" and "Zheng" groups in CASP15 for protein monomer and complex structure prediction. These prediction sets were obtained using the D-I-TASSER and DMFold-Multimer algorithms, respectively. For monomer structure pred...
Algorithms Deep Learning Software Protein Conformation Sequence Alignment Proteins Models, Molecular
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Development and validation of machine learning models for the prediction of SH-2 containing protein tyrosine phosphatase 2 inhibitors.

Molecular diversity Aug 8, 2023
Discovery and development of a new drug to the market is a highly challenging and resource consuming process. Although, modern drug discovery technologies have enabled the rapid identification of lead compounds, translation of the lead compounds into...
Protein Tyrosine Phosphatase, Non-Receptor Type 11 Drug Discovery Machine Learning Models, Molecular Reproducibility of Results Humans Enzyme Inhibitors Small Molecule Libraries
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AndroPred: an artificial intelligence-based model for predicting androgen receptor inhibitors.

Journal of biomolecular structure & dynamics Jul 26, 2023
Androgen receptor (AR), a steroid receptor, plays a pivotal role in the pathogenesis of prostate cancer (PCa). AR controls the transcription of genes that help cells avoid apoptosis and proliferate, thereby contributing to the development of PCa. Und...
Humans Artificial Intelligence Receptors, Androgen Machine Learning Models, Molecular Quantitative Structure-Activity Relationship Algorithms Prostatic Neoplasms Androgen Receptor Antagonists Male Drug Discovery
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Improving protein structure prediction with extended sequence similarity searches and deep-learning-based refinement in CASP15.

Proteins Jul 24, 2023
The human predictor team PEZYFoldings got first place with the assessor's formulae (3rd place with Global Distance Test Total Score [GDT-TS]) in the single-domain category and 10th place in the multimer category in Critical Assessment of Structure Pr...
Models, Molecular Protein Conformation Computational Biology Proteins Deep Learning Humans
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VoroIF-GNN: Voronoi tessellation-derived protein-protein interface assessment using a graph neural network.

Proteins Jul 21, 2023
We present VoroIF-GNN (Voronoi InterFace Graph Neural Network), a novel method for assessing inter-subunit interfaces in a structural model of a protein-protein complex, relying solely on the input structure without any additional information. Given ...
Models, Molecular Neural Networks, Computer Proteins
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Combining pairwise structural similarity and deep learning interface contact prediction to estimate protein complex model accuracy in CASP15.

Proteins Jun 26, 2023
Estimating the accuracy of quaternary structural models of protein complexes and assemblies (EMA) is important for predicting quaternary structures and applying them to studying protein function and interaction. The pairwise similarity between struct...
Deep Learning Proteins Models, Molecular
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A Simple Way to Incorporate Target Structural Information in Molecular Generative Models.

Journal of chemical information and modeling Jun 15, 2023
Deep learning generative models are now being applied in various fields including drug discovery. In this work, we propose a novel approach to include target 3D structural information in molecular generative models for structure-based drug design. Th...
Proteins Models, Molecular Drug Discovery Neural Networks, Computer Drug Design
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Residue-level error detection in cryoelectron microscopy models.

Structure (London, England : 1993) May 29, 2023
Building accurate protein models into moderate resolution (3-5 Å) cryoelectron microscopy (cryo-EM) maps is challenging and error prone. We have developed MEDIC (Model Error Detection in Cryo-EM), a robust statistical model that identifies local back...
Protein Conformation Proteins Cryoelectron Microscopy Machine Learning Models, Molecular
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ImmuneBuilder: Deep-Learning models for predicting the structures of immune proteins.

Communications biology May 29, 2023
Immune receptor proteins play a key role in the immune system and have shown great promise as biotherapeutics. The structure of these proteins is critical for understanding their antigen binding properties. Here, we present ImmuneBuilder, a set of de...
Single-Domain Antibodies Deep Learning Models, Molecular Receptors, Antigen, T-Cell Antibodies
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