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Structure Prediction Tools

Date	Name	Title	Target	Predicted property	Code/Server
12-Jun-26	PBCNet2.0	Atomic-level protein–ligand recognition with PBCNet2.0 for probe discovery	Binding affinity prediction	https://doi.org/10.1038/s41589-026-02241-x
08-Jul-25	PeptiTox	Integrating Protein Language Models and Geometric Deep Learning for Peptide Toxicity Prediction	Peptides	Peptide toxicity prediction	Link
15-Mar-25	DTIAM	DTIAM: a unified framework for predicting drug-target interactions, binding affinities and drug mechanisms	Small molecule	Multi-task framework for prediction of interaction, affinity, & mechanism	Link
05-Mar-25	AMP-Designer	Discovery of antimicrobial peptides with notable antibacterial potency by an LLM- based foundation model	AMPs	Peptide antimicrobial activity prediction	Link
04-Mar-25	PLAPD	Leveraging protein language models for robust antimicrobial peptide detection	AMPs	Peptide antimicrobial activity prediction	Link
18-Feb-25	T-ALPHA	T-ALPHA: A Hierarchical Transformer-Based Deep Neural Network for Protein?Ligand Binding Affinity Prediction with Uncertainty-Aware Self-Learning for Protein-Specific Alignment	Small molecule	Affinity prediction	Link
29-Jan-25	MutualDTA	MutualDTA: An Interpretable Drug?Target Affinity Prediction Model Leveraging Pretrained Models and Mutual Attention	Protein-small molecules	Affinity prediction	Link
29-Jan-25	pLM4CPPs	pLM4CPPs: Protein Language Model-Based Predictor for Cell Penetrating Peptides	Peptides	cell penetration prediction	Link
20-Jan-25	MMPD-DTA	MMPD-DTA: Integrating Multi-Modal Deep Learning with Pocket-Drug Graphs for Drug-Target Binding Affinity Prediction	Protein-small molecules	Affinity prediction	Link
17-Jan-25	EvoGradient	Explainable deep learning and virtual evolution identifies antimicrobial peptides with activity against multidrug-resistant human pathogens	AMPs	Peptide antimicrobial activity prediction	Link
16-Jan-25	MultiChem	MultiChem: predicting chemical properties using multi-view graph attention network	Small molecule	a framework for classification or regression tasks	Link
13-Jan-25	BlendNet	Exploring the potential of compound?protein complex structure-free models in virtual screening using BlendNet	Protein-small molecules	Affinity prediction	Link
11-Jan-25	UniAMP	UniAMP: enhancing AMP prediction using deep neural networks with inferred information of peptides	AMPs	Peptide antimicrobial activity prediction	Link
10-Jan-25	deep-AMPpred	deep-AMPpred: A Deep Learning Method for Identifying Antimicrobial Peptides and Their Functional Activities	AMPs	Peptide antimicrobial activity prediction	Link
16-Dec-24	MHAN-DTA	MHAN-DTA: A Multiscale Hybrid Attention Network for Drug-Target Affinity Prediction	Protein-small molecules	Affinity prediction	Link
11-Dec-24	PepMNet	PepMNet: a hybrid deep learning model for predicting peptide properties using hierarchical graph representations	AMPs	Peptide antimicrobial activity prediction	Link
01-Dec-24	GEMS	GEMS: A Generalizable GNN Framework For Protein-Ligand Binding Affinity Prediction Through Robust Data Filtering and Language Model Integration	Protein-small molecules	Affinity prediction	Link
28-Sep-24	PepNet	PepNet: an interpretable neural network for anti-inflammatory and antimicrobial peptides prediction using a pre-trained protein language model	AMPs	Peptide antimicrobial activity prediction	Link
30-Aug-24	deepAMP	A Foundation Model Identifies Broad-Spectrum Antimicrobial Peptides against Drug-Resistant Bacterial Infection	AMPs	Peptide antimicrobial activity prediction	Link
06-Aug-24	DMAMP	DMAMP: A Deep-Learning Model for Detecting Antimicrobial Peptides and Their Multi-Activities	AMPs	Peptide antimicrobial activity prediction	Link
17-Jul-24	TriStack	TriStack enables accurate identification of antimicrobial and anti-inflammatory peptides by combining machine learning and deep learning approaches	AMPs	Peptide antimicrobial activity prediction	Link
07-Jul-24	AMP	Ensemble Machine Learning and Predicted Properties Promote Antimicrobial Peptide Identification	AMPs	Peptide antimicrobial activity prediction	Link
26-Jun-24	TP-LMMSG	TP-LMMSG: a peptide prediction graph neural network incorporating flexible amino acid property representation	AMPs	Peptide antimicrobial activity prediction	Link
22-Jun-24	tAMPer	Structure-aware deep learning model for peptide toxicity prediction	AMPs	Peptide antimicrobial activity prediction	Link
05-Jun-24	AMP-RNNpro	AMP-RNNpro: a two-stage approach for identification of antimicrobials using probabilistic features	AMPs	Peptide antimicrobial activity prediction	Link
04-Jun-24	iAMP-DL	An efficient hybrid deep learning architecture for predicting short antimicrobial peptides	AMPs	Peptide antimicrobial activity prediction	Link
17-Feb-24	graphLambda	graphLambda: Fusion Graph Neural Networks for Binding Affinity Prediction	Small molecule	Affinity prediction	Link
04-Jan-24	MulinforCPI	MulinforCPI: enhancing precision of compound?protein interaction prediction through novel perspectives on multi-level information integration	Small molecule	Affinity prediction	Link
11-Dec-23	MBP	Multi-task bioassay pre-training for protein-ligand binding affinity prediction	Small molecule	Affinity prediction	Link
15-Mar-23	HydrAMP	Discovering highly potent antimicrobial peptides with deep generative model HydrAMP	AMPs	Peptide antimicrobial activity prediction	Link
10-Mar-23	TriNet	TriNet: A tri-fusion neural network for the prediction of anticancer and antimicrobial peptides	AMPs	Peptide antimicrobial activity prediction	Link
27-Feb-23	KreinAMP	Krein support vector machine classification of antimicrobial peptides	AMPs	Peptide antimicrobial activity prediction	Link
21-Dec-22	MoLFormer	Large-scale chemical language representations capture molecular structure and properties	LBVS	A pretrained-on-SMILES transformer that can be finetuned for downstream molecular property prediction	Link
07-Apr-22	TPpred-ATMV	TPpred-ATMV: therapeutic peptide prediction by adaptive multi-view tensor learning model	AMPs	Peptide antimicrobial activity prediction	Link
01-Feb-22	X-Mol	X-MOL: large-scale pre-training for molecular understanding and diverse molecular analysis	Small molecule	A pretrained-on-SMILES transformer that can be finetuned for downstream molecular property prediction	Link
25-Jan-22	AMPlify	AMPlify: attentive deep learning model for discovery of novel antimicrobial peptides effective against WHO priority pathogens	AMPs	Peptide antimicrobial activity prediction	Link
19-Oct-20	ChemBERTa	ChemBERTa: Large-Scale Self-Supervised Pretraining for Molecular Property Prediction	Small molecule	A pretrained-on-SMILES transformer that can be finetuned for downstream molecular property prediction	Link
30-Jul-19	Chemprop	Analyzing Learned Molecular Representations for Property Prediction	Small molecule	a framework for classification or regression tasks	Link