AIMC Topic: Computational Biology
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Reliable protein-protein docking with AlphaFold, Rosetta, and replica exchange.
eLife
May 27, 2025
Despite the recent breakthrough of AlphaFold (AF) in the field of protein sequence-to-structure prediction, modeling protein interfaces and predicting protein complex structures remains challenging, especially when there is a significant conformation...
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...
Novel Computational Approaches in the Discovery and Identification of Bioactive Peptides: A Bioinformatics Perspective.
Journal of agricultural and food chemistry
May 24, 2025
Bioactive peptides are protein molecules known for their specific biological functions, offering promising applications across various fields including medicine, food, and cosmetics. Traditional approaches to the investigation of bioactive peptides t...
Cell-TRACTR: A transformer-based model for end-to-end segmentation and tracking of cells.
PLoS computational biology
May 23, 2025
Deep learning-based methods for identifying and tracking cells within microscopy images have revolutionized the speed and throughput of data analysis. These methods for analyzing biological and medical data have capitalized on advances from the broad...
Identification of shared mechanisms between Alzheimer's disease and atherosclerosis by integrated bioinformatics analysis.
European journal of medical research
May 22, 2025
Alzheimer's disease (AD) and atherosclerosis (AS) are two interacting diseases mostly affecting aged adults. AD is characterized by the deposition of neuritic plaques mainly consisting of Aβ, and AS is defined by the formation of atheromatous plaque ...
Applying computational protein design to therapeutic antibody discovery - current state and perspectives.
Frontiers in immunology
May 22, 2025
Machine learning applications in protein sciences have ushered in a new era for designing molecules in silico. Antibodies, which currently form the largest group of biologics in clinical use, stand to benefit greatly from this shift. Despite the prol...
Transcriptomic insights into the mechanism of action of telomere-related biomarkers in rheumatoid arthritis.
Frontiers in immunology
May 22, 2025
BACKGROUND: Rheumatoid arthritis (RA) is an autoimmune inflammatory disease. The mechanism by which telomeres are involved in the development of RA remains unclear. This study aimed to investigate the relationship between RA and telomeres.
Evaluating methods for the prediction of cell-type-specific enhancers in the mammalian cortex.
Cell genomics
May 21, 2025
Identifying cell-type-specific enhancers is critical for developing genetic tools to study the mammalian brain. We organized the "Brain Initiative Cell Census Network (BICCN) Challenge: Predicting Functional Cell Type-Specific Enhancers from Cross-Sp...
CoupleMDA: Metapath-Induced Structural-Semantic Coupling Network for miRNA-Disease Association Prediction.
International journal of molecular sciences
May 21, 2025
The prediction of microRNA-disease associations (MDAs) is crucial for understanding disease mechanisms and biomarker discovery. While graph neural networks have emerged as promising tools for MDA prediction, existing methods face critical limitations...
RNAcare: integrating clinical data with transcriptomic evidence using rheumatoid arthritis as a case study.
BMC medical genomics
May 21, 2025
BACKGROUND: Gene expression analysis is a crucial tool for uncovering the biological mechanisms that underlie differences between patient subgroups, offering insights that can inform clinical decisions. However, despite its potential, gene expression...
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