AI	Artificial Intelligence
BindingDB	Binding Database
BioGRID	Biological General Repository for Interaction Datasets
BioLiP	Biologically Relevant Ligand–Protein Binding Interactions Database
BSA	Bovine Serum Albumin
CAFA	Critical Assessment of Protein Function Annotation
ChEMBL	Chemogenomic Database
CNN	Convolutional Neural Network
CNTs	Carbon Nanotubes
CSI	Cell Shape Index
DFT	Density Functional Theory
DIP	Database of Interacting Proteins
DL	Deep Learning
DNA	Deoxyribonucleic Acid
DNNs	Deep Neural Networks
DrugBank	Drug and Drug Target Database
DWCNTs	Doublewalled Carbon Nanotubes
ENMs	Engineered Nanomaterials
ERA	Environmental Risk Assessment
ERT	Extremely Randomized Tree
FAIR	Findable, Accessible, Interoperable, and Reusable
GBDT	Gradient-Boosting Decision Tree
GLASS	GPCR–Ligand Association
GO	Gene Ontology
GPCR	G-Protein-Coupled Receptor
GPCRdb	G-Protein-Coupled Receptor Database
His	Histidine
HPRD	Human Protein Reference Database
IntAct	Molecular Interaction Database
KGsim2vec	Knowledge-Graph-Based Method
KNN	K-Nearest Neighbor
LigAsite	Ligand Attachment Site Database
LightGBM	Light Gradient-Boosting Machine
LLMPs	Large Language Models for Proteins
MD	Molecular Dynamics
ML	Machine Learning
MWCNTs	Multiwalled Carbon Nanotubes
NAFs	Nuclear Area Factors
NBRP	NP Blood Removal Pathways
NMs	Nanomaterials
NN	Neural Networks
NPs	Nanoparticles
RPA	Relative Protein Abundance
PCRO-RLRM	Polypeptide Chemical Reaction Optimized Resistant Logistic Regression Model
PDB	Protein Data Bank
PDBbind	Binding Affinity Data for Biomolecular Complexes Deposited in the PDB
PepPIs/PPIs	Peptide/Protein–Protein Interactions
Phe	Phenylalanine
Phos	Phosphorylation
PLIs	Protein–Ligand Interactions
PSSM	Position-Specific Scoring Matrix
PPIs	Protein–Protein Interactions
QSAR	Quantitative Structure–Activity Relationship
PubChem	Public Chemical Information Resource
R2	Coefficient of Determination
RF	Random Forest
RNA	Ribonucleic Acid
SHAP	SHapley Additive exPlanations
SKEMPI	Structural Kinetic and Energetic Database of Mutant Protein Interactions
SOM	Self-Organizing Map
STRING	Search Tool for the Retrieval of Interacting Genes/Proteins
SVM	Support Vector Machine
Trp	Tryptophan
Tyr	Tyrosine
UMOD	Uromodulin
UniProt	Universal Protein Resource
XGBoost	Extreme Gradient Boosting