AIMC Topic: Models, Molecular

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AbEpiTope-1.0: Improved antibody target prediction by use of AlphaFold and inverse folding.

Science advances Jun 13, 2025
B cell epitope prediction tools are crucial for designing vaccines and disease diagnostics. However, predicting which antigens a specific antibody binds to and their exact binding sites (epitopes) remains challenging. Here, we present AbEpiTope-1.0, ...
Software Computational Biology Models, Molecular Humans Machine Learning Epitopes, B-Lymphocyte Antigen-Antibody Complex Antibodies Protein Folding Antigens
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MlCOFSyn: A Machine Learning Framework To Facilitate the Synthesis of 2D Covalent Organic Frameworks.

Journal of chemical information and modeling Jun 5, 2025
Two-dimensional covalent organic frameworks (2D COFs) have been historically synthesized empirically, often resulting in uncontrolled crystallization and inferior crystal sizes, which limit their performance in various applications. Recently, crystal...
Machine Learning Metal-Organic Frameworks Crystallization Models, Molecular Chemistry Techniques, Synthetic
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Amortized template matching of molecular conformations from cryoelectron microscopy images using simulation-based inference.

Proceedings of the National Academy of Sciences of the United States of America Jun 4, 2025
Characterizing the conformational ensemble of biomolecular systems is key to understand their functions. Cryoelectron microscopy (cryo-EM) captures two-dimensional snapshots of biomolecular ensembles, giving in principle access to thermodynamics. How...
Molecular Conformation Cryoelectron Microscopy Models, Molecular Bayes Theorem Neural Networks, Computer Deep Learning Image Processing, Computer-Assisted Computer Simulation
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Modeling Active-State Conformations of G-Protein-Coupled Receptors Using AlphaFold2 via Template Bias and Explicit Protein Constrains.

Journal of chemical information and modeling May 29, 2025
AlphaFold2 and other deep learning tools represent the state of the art for protein structure prediction; however, they are still limited in their ability to model multiple protein conformations. Since the function of many proteins depends on their a...
Ligands Protein Conformation Receptors, G-Protein-Coupled Models, Molecular Humans Deep Learning
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Automating the Analysis of Substrate Reactivity through Environment Interaction Mapping.

Journal of chemical information and modeling May 28, 2025
Exploring the interaction configurations between substrates and atomic or molecular systems is crucial for various scientific and technological applications, such as characterizing catalytic reactions, solvation structures, and molecular interactions...
Models, Molecular Automation Machine Learning Cluster Analysis
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EMOCPD: Efficient Attention-Based Models for Computational Protein Design Using Amino Acid Microenvironment.

Journal of chemical information and modeling May 26, 2025
Computational protein design (CPD) refers to the use of computational methods to design proteins. Traditional methods relying on energy functions and heuristic algorithms for sequence design are inefficient and do not meet the demands of the big data...
Protein Conformation Protein Engineering Computational Biology Models, Molecular Amino Acids Proteins
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Cyclic peptide structure prediction and design using AlphaFold2.

Nature communications May 21, 2025
Small cyclic peptides have gained significant traction as a therapeutic modality; however, the development of deep learning methods for accurately designing such peptides has been slow, mostly due to the lack of sufficiently large training sets. Here...
Deep Learning Computational Biology Models, Molecular Amino Acid Sequence Humans Drug Design Kelch-Like ECH-Associated Protein 1 Protein Conformation Peptides, Cyclic Proto-Oncogene Proteins c-mdm2 Crystallography, X-Ray
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DihedralsDiff: A Diffusion Conformation Generation Model That Unifies Local and Global Molecular Structures.

Journal of chemical information and modeling May 20, 2025
Significant advancements have been made in utilizing artificial intelligence to learn to generate molecular conformations, which has greatly facilitated the discovery of drug molecules. In particular, the rapid development of diffusion models has led...
Diffusion Molecular Conformation Models, Molecular
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Structural Biology in the AlphaFold Era: How Far Is Artificial Intelligence from Deciphering the Protein Folding Code?

Biomolecules May 6, 2025
Proteins are biomolecules characterized by uncommon chemical and physicochemical complexities coupled with extreme responsiveness to even minor chemical modifications or environmental variations. Since the shape that proteins assume is fundamental fo...
Machine Learning Computational Biology Humans Protein Conformation Proteins Artificial Intelligence Protein Folding Models, Molecular
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M-DeepAssembly: enhanced DeepAssembly based on multi-objective multi-domain protein conformation sampling.

BMC bioinformatics May 5, 2025
BACKGROUND: Association and cooperation among structural domains play an important role in protein function and drug design. Despite remarkable advancements in highly accurate single-domain protein structure prediction through the collaborative effor...
Databases, Protein Computational Biology Models, Molecular Algorithms Protein Domains Deep Learning Proteins Protein Conformation
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