Research Articles
Beyond RMSD: A Comprehensive Guide to Using lDDT and pLDDT for Validating Protein Structure Predictions
This article provides researchers, scientists, and drug development professionals with a comprehensive guide to the Local Distance Difference Test (lDDT) and its predicted variant, pLDDT.
How to Calculate RMSD for Protein Structure Comparison: A Guide for Structural Biologists and Drug Developers
This article provides a comprehensive guide to calculating and interpreting the Root Mean Square Deviation (RMSD) for protein structure comparison, a fundamental task in structural biology, drug discovery, and protein...
Benchmarking Protein Structure Prediction Tools: From Monomeric Accuracy to Complex Challenges in Biomedical Research
This article provides a comprehensive benchmarking analysis of modern protein structure prediction tools, addressing critical needs for researchers, scientists, and drug development professionals.
CASP Experiment: The Gold Standard in Protein Structure Prediction
This article provides a comprehensive overview of the Critical Assessment of protein Structure Prediction (CASP), the community-wide experiment that has driven progress in computational biology for three decades.
Validating Protein Structure Prediction for Snake Venom Toxins: From Computational Models to Therapeutic Applications
This article provides a comprehensive overview of the validation of protein structure prediction tools for snake venom toxins, a diverse and challenging class of proteins.
Benchmarking Multimer Prediction Tools: A Comprehensive Guide to Accuracy, Applications, and Future Directions
Accurately predicting the structure of multimeric protein complexes is a cornerstone of modern biology, with profound implications for understanding disease mechanisms and accelerating drug discovery.
Homology Modeling Programs in 2025: A Comprehensive Performance Review for Drug Discovery and Structural Biology
This article provides a contemporary analysis of the performance and practical application of homology modeling programs, a cornerstone technique in computational biology.
Deep Learning in Protein Structure Prediction: A Comprehensive Comparison of AlphaFold, RoseTTAFold, and Emerging Methods
This article provides a comprehensive analysis of modern deep learning methods for protein structure prediction, tailored for researchers and drug development professionals.
Benchmarking Protein Structure Prediction Servers: From AlphaFold to DeepSCFold
This article provides a comprehensive guide for researchers and drug development professionals on the critical evaluation of protein structure prediction servers.
Template-Free vs. Template-Based Protein Structure Prediction: A Comprehensive Accuracy Benchmark for Biomedical Research
This article provides a critical evaluation of template-based and template-free computational methods for predicting protein structures, a cornerstone of modern drug discovery.