PATH has state-of-the-art performance versus previous binding affinity prediction algorithms. by Yuxi Long (11024307)

Subjects:

PATH⁺ explains tighter binding of carbonic anhydrase II by brinzolamide. by Yuxi Long (11024307)

Subjects:

PATH (with persistence fingerprint) runs significantly faster than TNet-BP, a representative binding affinity prediction algorithm that uses persistent homology, on larger protein-ligand complexes. by Yuxi Long (11024307)

Subjects:

Visualization by PaCMAP [52] shows that persistence fingerprint clusters protein-ligand complexes with similar binding affinity reasonably well, even beyond the training dataset (P... by Yuxi Long (11024307)

Subjects:

Scatter plots of PATH⁺ and our implementation of TNet-BP’s predictions on a held-out, test subset of PDBBind v2020 refined set for one run (90:10 train:test split ratio,... by Yuxi Long (11024307)

Subjects:

PATH⁺ correctly predicted a weaker binding affinity for HIV-1 protease with the drug-resistant G48V mutation (right, experimental kcal/mol, PDB ID: 3cyw [81]) bound to d... by Yuxi Long (11024307)

Subjects:

An overview of PATH⁺. by Yuxi Long (11024307)

Subjects:

The 10 features captured by persistence fingerprint. by Yuxi Long (11024307)

Subjects:

^aTwo HIV-1 protease mutants bound to inhibitor darunavir (G48V: PDB ID 3cyw [81] & L90M: PDB ID 2f81 [82]). by Yuxi Long (11024307)

Subjects:

Two protein-ligand complexes shown with their persistence fingerprint. by Yuxi Long (11024307)

Subjects:

Performance of TNet-BP and PATH⁺ on the PDBBind v2020 refined set shows that PATH⁺ achieves similar performance with TNet-BP while having three orders fewer f... by Yuxi Long (11024307)

Subjects:

Construction of internuclear persistence contours (IPCs). by Yuxi Long (11024307)

Subjects:

Comparison of PATH⁺ with TNet-BP [43]. by Yuxi Long (11024307)

Subjects:

Previously literatures on feature evaluation for relevance based on linear transformation. by Jia Liu (41593)

Main code. by Jingguo Bi (21439766)

Calculated importance of the features selected based on relevance to MQI. by Naiara Virto (20490408)

Relevant Parameters. by Dongyan Wang (195482)

Relevant computed image data. by Zhaoyu Ku (20660546)

List of technical characteristics of relevant literature. by Haoran Cui (7235234)

MHC II binding predictions by Robert Sinkovits (8918225)

“…<p dir="ltr">Predictions of peptide (15-mer) bindings to mouse I-A^b MHCII molecule using the neural network algorithm implemented in the IEDB MHC II version 2.13 collection of tools [1]. …”