AIMC Topic: Protein Domains

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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...
Algorithms Deep Learning Models, Molecular Protein Domains Protein Conformation Computational Biology Proteins Databases, Protein
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Dual-Site Targeting by Peptide Inhibitors of the N-Terminal Domain of Hsp90: Mechanism and Design.

Journal of chemical information and modeling May 1, 2025
Heat shock protein 90 (Hsp90) is a pivotal molecular chaperone crucial in the maturation of client proteins, positioning it as a significant target for cancer therapy. However, the design of effective Hsp90 inhibitors presents substantial challenges ...
Protein Binding Protein Domains Molecular Dynamics Simulation Adenosine Triphosphate Binding Sites HSP90 Heat-Shock Proteins Peptides Molecular Docking Simulation Drug Design Humans Machine Learning
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Simpler Protein Domain Identification Using Spectral Clustering.

Proteins Feb 13, 2025
The decomposition of a biomolecular complex into domains is an important step to investigate biological functions and ease structure determination. A successful approach to do so is the SPECTRUS algorithm, which provides a segmentation based on spect...
Cluster Analysis Proteins Databases, Protein Algorithms Deep Learning Computational Biology Protein Conformation Sequence Alignment Sequence Analysis, Protein Models, Molecular Protein Domains Amino Acid Sequence
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Lessons from Deep Learning Structural Prediction of Multistate Multidomain Proteins-The Case Study of Coiled-Coil NOD-like Receptors.

International journal of molecular sciences Jan 9, 2025
We test here the prediction capabilities of the new generation of deep learning predictors in the more challenging situation of multistate multidomain proteins by using as a case study a coiled-coil family of Nucleotide-binding Oligomerization Domain...
Protein Structure, Secondary Arabidopsis Protein Domains Protein Conformation Deep Learning Computational Biology Models, Molecular NLR Proteins
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DPFunc: accurately predicting protein function via deep learning with domain-guided structure information.

Nature communications Jan 2, 2025
Computational methods for predicting protein function are of great significance in understanding biological mechanisms and treating complex diseases. However, existing computational approaches of protein function prediction lack interpretability, mak...
Protein Conformation Models, Molecular Protein Domains Algorithms Deep Learning Computational Biology Proteins Databases, Protein Structure-Activity Relationship Humans
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Rational design of potent phosphopeptide binders to endocrine Snk PBD domain by integrating machine learning optimization, molecular dynamics simulation, binding energetics rescoring, and in vitro affinity assay.

European biophysics journal : EBJ Nov 29, 2024
Human Snk is an evolutionarily conserved serine/threonine kinase essential for the maintenance of endocrine stability. The protein consists of a N-terminal catalytic domain and a C-terminal polo-box domain (PBD) that determines subcellular localizati...
Thermodynamics Phosphopeptides Molecular Dynamics Simulation Amino Acid Sequence Protein Binding Humans Protein Serine-Threonine Kinases Machine Learning Protein Domains Drug Design
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Deciphering Cas9 specificity: Role of domain dynamics and RNA:DNA hybrid interactions revealed through machine learning and accelerated molecular simulations.

International journal of biological macromolecules Nov 19, 2024
CRISPR/Cas9 technology is widely used for gene editing, but off-targeting still remains a major concern in therapeutic applications. Although Cas9 variants with better mismatch discrimination have been developed, they have significantly lower rates o...
Substrate Specificity CRISPR-Associated Protein 9 DNA Francisella CRISPR-Cas Systems Machine Learning Bacterial Proteins Protein Domains Molecular Dynamics Simulation RNA
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Exploring structural diversity across the protein universe with The Encyclopedia of Domains.

Science (New York, N.Y.) Nov 1, 2024
The AlphaFold Protein Structure Database (AFDB) contains more than 214 million predicted protein structures composed of domains, which are independently folding units found in multiple structural and functional contexts. Identifying domains can enabl...
Protein Domains Deep Learning Protein Folding Proteins Databases, Protein
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Deep learning for discriminating non-trivial conformational changes in molecular dynamics simulations of SARS-CoV-2 spike-ACE2.

Scientific reports Sep 30, 2024
Molecular dynamics (MD) simulations produce a substantial volume of high-dimensional data, and traditional methods for analyzing these data pose significant computational demands. Advances in MD simulation analysis combined with deep learning-based a...
Protein Conformation Angiotensin-Converting Enzyme 2 Binding Sites COVID-19 Protein Domains SARS-CoV-2 Molecular Dynamics Simulation Deep Learning Protein Binding Humans Spike Glycoprotein, Coronavirus Mutation
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A Machine Learning Approach to Identify C Type Lectin Domain (CTLD) Containing Proteins.

The protein journal Jul 28, 2024
Lectins are sugar interacting proteins which bind specific glycans reversibly and have ubiquitous presence in all forms of life. They have diverse biological functions such as cell signaling, molecular recognition, etc. C-type lectins (CTL) are a gro...
Humans Lectins, C-Type Protein Domains Machine Learning
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