Artificial intelligence in the prediction of proteinligand interactions: recent advances and future directions

A Dhakal, C McKay, JJ Tanner… - Briefings in …, 2022 - academic.oup.com
… compared, themes identified, and gaps noted, and suggestions recommended … prediction
results of known scoring functions allowing a fair comparison of the model with existing scoring

Featurization strategies for proteinligand interactions and their applications in scoring function development

G Xiong, C Shen, Z Yang, D Jiang, S Liu… - Wiley …, 2022 - Wiley Online Library
… The authors attributed the success of NNScore to its integration strategy in feature extraction…
), the energy difference between those orbitals (E GAP ), electronegativity (χ), and so on. The …

[HTML][HTML] Scoring functions for protein-ligand binding affinity prediction using structure-based deep learning: a review

R Meli, GM Morris, PC Biggin - Frontiers in bioinformatics, 2022 - frontiersin.org
… The success of supervised machine learning and deep … In this way, protein-ligand interactions
are encoded implicitly … The authors highlight a significant performance gap between in-…

Proteinprotein docking: Past, present, and future

S Sunny, PB Jayaraj - The protein journal, 2022 - Springer
… a considerable gap between the number of individual protein … This addition made a drastic
increase in the success rate of … the scoring phase precisely determine the quality of predictions

Machine learning and ligand binding predictions: a review of data, methods, and obstacles

SR Ellingson, B Davis, J Allen - … et Biophysica Acta (BBA)-General Subjects, 2020 - Elsevier
… The ability to accurately predict protein-ligand interactions … The success of these models is
typically measured in dataset … This gap gets smaller with aofb, but still exists. Strangely, the …

Improving proteinligand docking and screening accuracies by incorporating a scoring function correction term

L Zheng, J Meng, K Jiang, H Lan, Z Wang… - Briefings in …, 2022 - academic.oup.com
… redocking and cross-docking success rates, indicating that it … and distance gap between
shells (14 shells and distance gap of … He is working on protein-ligand interaction prediction and …

Machine learning on ligand-residue interaction profiles to significantly improve binding affinity prediction

B Ji, X He, J Zhai, Y Zhang, VH Man… - Briefings in …, 2021 - academic.oup.com
… used to characterize the proteinligand complex in an ML-… , RF-score, with the application of
RF to predict proteinligand binding … We calculated the MM-GBSA residue-ligand interaction

A new paradigm for applying deep learning to proteinligand interaction prediction

Z Wang, S Wang, Y Li, J Guo, Y Wei, Y Mu… - Briefings in …, 2024 - academic.oup.com
… structures predicted by AlphaFold2, the overall top 1 success … began to directly predict the
RMSD of docking poses (such … [38]), or use scores from other mathematical spaces (such as …

Scoring of proteinprotein docking models utilizing predicted interface residues

G Pozzati, P Kundrotas… - Proteins: Structure …, 2022 - Wiley Online Library
… in the docking success when applying interface predictions to the scoring of the docking
poses. … A large performance gap can be observed with different contact prediction methods. …

[HTML][HTML] Ssnet: A deep learning approach for protein-ligand interaction prediction

N Verma, X Qu, F Trozzi, M Elsaied, N Karki… - International journal of …, 2021 - mdpi.com
… based [5] PLI predictions, have been developed, with limited success. Often, these methods
… of docking scores obtained from each docking method. For each target, the docking scores