De Novo Design Tools
AMP_ML
Date: 13-Feb-24
Paper: Accelerating Antimicrobial Peptide Discovery for WHO Priority Pathogens through Predictive and Interpretable Machine Learning Models
Task: A series of models to predict AMPs and toxicity
DOI: https://doi.org/10.1021/acsomega.3c08676
Code: https/github.com/LCCBTsai/AMP_ML
AlphaPulldown
Date: 22-Dec-22
Paper: AlphaPulldown?a python package for protein?protein interaction screens using AlphaFold-Multimer
Task: As the name suggest, it predicts which proteins are likely to interact with a bait protein
DOI: https://doi.org/10.1093/bioinformatics/btac749
Code: https://github.com/KosinskiLab/AlphaPulldown
PoseCheck
Date: 28-Oct-23
Paper: PoseCheck: Generative Models for 3D Structure-based Drug Design Produce Unrealistic Poses
Task: Benchmark
DOI: https://www.mlsb.io/papers_2023/PoseCheck_Generative_Models_for_3D_Structure-based_Drug_Design_Produce_Unrealistic_Poses.pdf
Code: https://github.com/cch1999/posecheck
ABCFold
Date: 18-Mar-25
Paper: ABCFold: easier running and comparison of AlphaFold 3, Boltz-1 and Chai-1
Task: Benchmark
DOI: https://doi.org/10.1101/2025.03.12.642791
Code: https://github.com/rigdenlab/ABCFold
PepPCBench
Date: 13-Apr-25
Paper: PepPCBench is a Comprehensive Benchmark for Protein-Peptide Complex Structure Prediction with AlphaFold3
Task: Benchmark
DOI: https://doi.org/10.1101/2025.04.08.647699
Code: https://github.com/zhaisilong/PepPCBench
Dedenser
Date: 30-Jan-25
Paper: Dedenser: A Python Package for Clustering and Downsampling Chemical Libraries
Task: Chemical libraries (small molecules) clustering and sampling
DOI: https://doi.org/10.1021/acs.jcim.4c01980
Code: https://github.com/MSDLLCpapers/dedenser
PyAMPAÿ
Date: 27-Jun-24
Paper: PyAMPA: a high-throughput prediction and optimization tool for antimicrobial peptides
Task: Discovery and optimization of AMPs
DOI: https://doi.org/10.1128/msystems.01358-23
Code: https://github.com/SysBioUAB/PyAMPA
DeepMSA
Date: 18-Nov-19
Paper: DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins
Task: Generates multiple sequence alignments
DOI: https://doi.org/10.1093/bioinformatics/btz863
Code: https://seq2fun.dcmb.med.umich.edu//DeepMSA/
ATOMICA
Date: 8-Apr-25
Paper: ATOMICA: Learning Universal Representations of Intermolecular Interactions
Task: Interactions representation
DOI: https://doi.org/10.1101/2025.04.02.646906
Code: https://github.com/mims-harvard/ATOMICA
PharmRL
Date: 31-Dec-24
Paper: PharmRL: pharmacophore elucidation with deep geometric reinforcement learning
Task: It generates a structure-based pharmacophore
DOI: https://doi.org/10.1186/s12915-024-02096-5
Code: https://github.com/RishalAggarwal/Pharmrl
ProteinMAE
Date: 29-Nov-23
Paper: ProteinMAE: masked autoencoder for protein surface self-supervised learning
Task: It learns protein surface features to predict binding sites
DOI: https://doi.org/10.1093/bioinformatics/btad724
Code: https://github.com/phdymz/ProteinMAE
HydraScreen
Date: 22-Jul-24
Paper: HydraScreen: A Generalizable Structure-Based Deep Learning Approach to Drug Discovery
Task: ML scoring function for poses and affinity
DOI: https://doi.org/10.1021/acs.jcim.4c00481
Code: https://github.com/Ro5-ai/hydrascreen
Diff-AMP
Date: 25-Jan-22
Paper: Diff-AMP: tailored designed antimicrobial peptide framework with all-in-one generation, identification, prediction and optimization
Task: Multi-task to generates, identifies, & optimizes AMPs
DOI: https://doi.org/10.1093/bib/bbae078
Code: https://github.com/wrab12/diff-amp
VN-EGNN
Date: 10-Apr-24
Paper: VN-EGNN: E(3)-Equivariant Graph Neural Networks with Virtual Nodes Enhance Protein Binding Site Identification
Task: Pocket identification
DOI: https://doi.org/10.48550/arXiv.2404.07194
Code: https://github.com/ml-jku/vnegnn
HSSPPI
Date: 4-Mar-25
Paper: HSSPPI: hierarchical and spatial-sequential modeling for PPIs prediction
Task: Protein-Protein interaction prediction
DOI: https://doi.org/10.1093/bib/bbaf079
Code: https://github.com/biolushuai/Hierarchical-Spatial-Sequential-Modeling-of-Protein
CSM-Potential2
Date: 23-Oct-23
Paper: CSM-Potential2: A comprehensive deep learning platform for the analysis of protein interacting interfaces
Task: Prediction of protein interaction interfaces with proteins, nucleic acids, and ligands
DOI: https://doi.org/10.1002/prot.26615
Code: https://biosig.lab.uq.edu.au/csm_potential/
LEGOLAS
Date: 10-Apr-25
Paper: LEGOLAS: A Machine Learning Method for Rapid and Accurate Predictions of Protein NMR Chemical Shifts
Task: Predicts different chemical shifts from sequences
DOI: https://doi.org/10.1021/acs.jctc.5c00026
Code: https://github.com/roitberg-group/legolas
DeepSurf
Date: 20-Jan-21
Paper: A surface-based deep learning approach for the prediction of ligand binding sites on proteins
Task: Predicts ligand binding site on protein surfaces
DOI: https://doi.org/10.1093/bioinformatics/btab009
Code: https://github.com/stemylonas/DeepSurf
PUResNetV2.0
Date: 7-Jul-24
Paper: PUResNetV2.0: a deep learning model leveraging sparse representation for improved ligand binding site prediction
Task: Predicts ligand binding site on protein surfaces
DOI: https://doi.org/10.1186/s13321-024-00865-6
Code: https://github.com/jivankandel/PUResNetV2.0
TPepPro
Date: 25-Nov-24
Paper: TPepPro: a deep learning model for predicting peptide?protein interactions
Task: Predicts protein-peptide interactions
DOI: https://doi.org/10.1093/bioinformatics/btae708
Code: https://github.com/wanglabhku/TPepPro
sAMPpred-GAT
Date: 7-Nov-22
Paper: sAMPpred-GAT: prediction of antimicrobial peptide by graph attention network and predicted peptide structure
Task: Predicts the activity & the structure of AMPs
DOI: https://doi.org/10.1093/bioinformatics/btac715
Code: https://github.com/HongWuL/sAMPpred-GAT
ZHMolGraph
Date: 16-Feb-25
Paper: RNA-protein interaction prediction using network-guided deep learning
Task: Protein & RNA interaction prediction
DOI: https://doi.org/10.1038/s42003-025-07694-9
Code: https://github.com/Zhaolab-GitHub/ZHMolGraph
Prop3D
Date: 4-Jan-24
Paper: Prop3D: A flexible, Python-based platform for machine learning with protein structural properties and biophysical data
Task: protein 3D Generate structural data for ML and DL
DOI: https://doi.org/10.1186/s12859-023-05586-5
Code: https://github.com/bouralab/Prop3D
PSICHIC
Date: 17-Jun-24
Paper: Physicochemical graph neural network for learning protein?ligand interaction fingerprints from sequence data
Task: Protein ligand interaction prediction
DOI: https://doi.org/10.1038/s42256-024-00847-1
Code: https://github.com/huankoh/PSICHIC
DeepGlycanSite
Date: 17-Jun-24
Paper: Highly accurate carbohydrate-binding site prediction with DeepGlycanSite
Task: Prediction of carbohydrate-binding sites on a protein
DOI: https://doi.org/10.1038/s41467-024-49516-2
Code: https://github.com/xichengeva/DeepGlycanSite
EnrichRBP
Date: 13-Jan-25
Paper: EnrichRBP: an automated and interpretable computational platform for predicting and analyzing RNA-binding protein events
Task: RBPs
DOI: https://doi.org/10.1093/bioinformatics/btaf018
Code: https://github.com/wangyb97/EnrichRBP
PRA-MutPred
Date: 23-Jan-25
Paper: PRA-MutPred: Predicting the Effect of Point Mutations in Protein?RNA Complexes Using Structural Features
Task: Mutation effect in RBPs
DOI: https://doi.org/10.1021/acs.jcim.4c01452
Code: https://web.iitm.ac.in/bioinfo2/pramutpred/index.html
NesT-NABind
Date: 17-Jan-25
Paper: NesT-NABind: a Nested Transformer for Nucleic Acid-Binding Site Prediction on Protein Surface
Task: RBPs predict RNA binding region
DOI: https://doi.org/10.1021/acs.jcim.4c01765
Code: https://github.com/Xinyue-M/NesTNA-Bind
EuDockScore
Date: 23-Oct-24
Paper: EuDockScore: Euclidean graph neural networks for scoring protein?protein interfaces
Task: Scoring functions to rank PPI interfaces as near native
DOI: https://doi.org/10.1093/bioinformatics/btae636
Code: https://gitlab.com/mcfeemat/eudockscore
MolE
Date: 10-Apr-25
Paper: Pre-trained molecular representations enable antimicrobial discovery
Task: Self-supervised representation learning of small molecules
DOI: https://doi.org/10.1038/s41467-025-58804-4
Code: https://github.com/rolayoalarcon/MolE
DrugAssist
Date: 3-Jan-25
Paper: DrugAssist: a large language model for molecule optimization
Task: Small molecule optimization
DOI: https://doi.org/10.1093/bib/bbae693
Code: https://github.com/blazerye/DrugAssist
DiffPhore
Date: 6-Mar-25
Paper: Knowledge-guided diffusion model for 3D ligand-pharmacophore mapping
Task: Small molecules pharmacophore
DOI: https://doi.org/10.1038/s41467-025-57485-3
Code: https://github.com/VicFisher/DiffPhore