AIMC Topic: Protein Multimerization

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Editorial-Sequences and topology.

Current opinion in structural biology Jun 4, 2017
Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Protein Interaction Mapping Protein Multimerization Protein Interaction Domains and Motifs Animals Molecular Docking Simulation Protein Binding Computational Biology Proteins Binding Sites Thermodynamics Humans Machine Learning
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Predicting protein conformational changes for unbound and homology docking: learning from intrinsic and induced flexibility.

Proteins Dec 5, 2016
Predicting protein conformational changes from unbound structures or even homology models to bound structures remains a critical challenge for protein docking. Here we present a study directly addressing the challenge by reducing the dimensionality a...
Protein Multimerization Structural Homology, Protein Dimensional Measurement Accuracy Binding Sites Thermodynamics Molecular Docking Simulation Protein Binding Computational Biology Models, Statistical Proteins Benchmarking Protein Conformation Machine Learning Software Research Design
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GGIP: Structure and sequence-based GPCR-GPCR interaction pair predictor.

Proteins Jun 8, 2016
G Protein-Coupled Receptors (GPCRs) are important pharmaceutical targets. More than 30% of currently marketed pharmaceutical medicines target GPCRs. Numerous studies have reported that GPCRs function not only as monomers but also as homo- or hetero-d...
Mice Support Vector Machine Databases, Protein Receptors, G-Protein-Coupled Area Under Curve Models, Molecular Amino Acid Sequence Humans Animals ROC Curve Protein Binding Binding Sites Protein Interaction Domains and Motifs Protein Structure, Secondary Protein Multimerization
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idDock+: Integrating Machine Learning in Probabilistic Search for Protein-Protein Docking.

Journal of computational biology : a journal of computational molecular cell biology Jul 29, 2015
Predicting the three-dimensional native structures of protein dimers, a problem known as protein-protein docking, is key to understanding molecular interactions. Docking is a computationally challenging problem due to the diversity of interactions an...
Protein Conformation Protein Binding Binding Sites Protein Multimerization Computational Biology Machine Learning Proteins Algorithms Ligands Molecular Docking Simulation
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The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning.

Nature communications Jan 27, 2015
The study of biomolecular interactions between a drug and its biological target is of paramount importance for the design of novel bioactive compounds. In this paper, we report on the use of molecular dynamics (MD) simulations and machine learning to...
Thermodynamics Pyrrolidines Protein Multimerization Purine-Nucleoside Phosphorylase Molecular Dynamics Simulation Ligands Pyrimidinones Humans Time Factors Machine Learning Protein Binding Algorithms Cluster Analysis Kinetics
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Machine Learning of Molecular Dynamics Simulations Provides Insights into the Modulation of Viral Capsid Assembly.

Journal of chemical information and modeling May 26, 2025
An effective approach in the development of novel antivirals is to target the assembly of viral capsids by using capsid assembly modulators (CAMs). CAMs targeting hepatitis B virus (HBV) have two major modes of function: they can either accelerate nu...
Machine Learning Virus Assembly Capsid Proteins Capsid Protein Multimerization Hepatitis B virus Molecular Dynamics Simulation Protein Conformation
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Integrating different approaches for the identification of new disruptors of HIV-1 capsid multimerization.

Biochemical and biophysical research communications May 12, 2025
Human Immunodeficiency Virus (HIV) belongs to the Lentivirus genus, Retroviridae family, enveloped by a lipid bilayer within which the capsid protein encases the viral genome, reverse transcriptase, and integrase proteins, key components for viral re...
Humans HIV Infections Anti-HIV Agents HIV-1 Capsid Proteins Capsid Protein Multimerization
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Machine learning-driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins.

Proceedings of the National Academy of Sciences of the United States of America Jan 4, 2022
RAS is a signaling protein associated with the cell membrane that is mutated in up to 30% of human cancers. RAS signaling has been proposed to be regulated by dynamic heterogeneity of the cell membrane. Investigating such a mechanism requires near-at...
Humans Cell Membrane Machine Learning Protein Multimerization Proto-Oncogene Proteins p21(ras) Signal Transduction Lipids Molecular Dynamics Simulation
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Accurate prediction of inter-protein residue-residue contacts for homo-oligomeric protein complexes.

Briefings in bioinformatics Sep 2, 2021
Protein-protein interactions play a fundamental role in all cellular processes. Therefore, determining the structure of protein-protein complexes is crucial to understand their molecular mechanisms and develop drugs targeting the protein-protein inte...
Binding Sites Protein Multimerization Protein Interaction Domains and Motifs Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Deep Learning Protein Binding Humans Proteins Datasets as Topic Software Molecular Docking Simulation
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Computational Models for Self-Interacting Proteins Prediction.

Protein and peptide letters Jan 1, 2020
Self-Interacting Proteins (SIPs), whose two or more copies can interact with each other, have significant roles in cellular functions and evolution of Protein Interaction Networks (PINs). Knowing whether a protein can act on itself is important to un...
Machine Learning Computer Simulation Proteins Databases, Protein Models, Molecular Protein Multimerization Drug Design Protein Interaction Maps Protein Binding
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