Other Tools

Date	Name	Title	What it does	Code/Server
23-Nov-25	RNAdvisor 2	RNAdvisor 2: A unified platform for RNA 3D model quality assessment using metrics, scoring functions, and meta-metrics	Quality analysis of RNA 3D structures	Link
04-Jul-25	MIC	MIC: A deep learning tool for assigning ions and waters in cryo-EM and crystal structures	Predicts if the site is for water molecule or ions	Link
13-Apr-25	PepPCBench	PepPCBench is a Comprehensive Benchmark for Protein-Peptide Complex Structure Prediction with AlphaFold3	Benchmark	Link
10-Apr-25	LEGOLAS	LEGOLAS: A Machine Learning Method for Rapid and Accurate Predictions of Protein NMR Chemical Shifts	Predicts different chemical shifts from sequences	Link
10-Apr-25	MolE	Pre-trained molecular representations enable antimicrobial discovery	Self-supervised representation learning of small molecules	Link
08-Apr-25	ATOMICA	ATOMICA: Learning Universal Representations of Intermolecular Interactions	Interactions representation	Link
18-Mar-25	ABCFold	ABCFold: easier running and comparison of AlphaFold 3, Boltz-1 and Chai-1	Benchmark	Link
06-Mar-25	DiffPhore	Knowledge-guided diffusion model for 3D ligand-pharmacophore mapping	Small molecules pharmacophore	Link
04-Mar-25	HSSPPI	HSSPPI: hierarchical and spatial-sequential modeling for PPIs prediction	Protein-Protein interaction prediction	Link
16-Feb-25	ZHMolGraph	RNA-protein interaction prediction using network-guided deep learning	Protein & RNA interaction prediction	Link
30-Jan-25	Dedenser	Dedenser: A Python Package for Clustering and Downsampling Chemical Libraries	Chemical libraries (small molecules) clustering and sampling	Link
23-Jan-25	PRA-MutPred	PRA-MutPred: Predicting the Effect of Point Mutations in Protein?RNA Complexes Using Structural Features	Mutation effect in RBPs	Link
17-Jan-25	NesT-NABind	NesT-NABind: a Nested Transformer for Nucleic Acid-Binding Site Prediction on Protein Surface	RBPs predict RNA binding region	Link
13-Jan-25	EnrichRBP	EnrichRBP: an automated and interpretable computational platform for predicting and analyzing RNA-binding protein events	RBPs	Link
03-Jan-25	DrugAssist	DrugAssist: a large language model for molecule optimization	Small molecule optimization	Link
31-Dec-24	PharmRL	PharmRL: pharmacophore elucidation with deep geometric reinforcement learning	It generates a structure-based pharmacophore	Link
25-Nov-24	TPepPro	TPepPro: a deep learning model for predicting peptide?protein interactions	Predicts protein-peptide interactions	Link
23-Oct-24	EuDockScore	EuDockScore: Euclidean graph neural networks for scoring protein?protein interfaces	Scoring functions to rank PPI interfaces as near native	Link
22-Jul-24	HydraScreen	HydraScreen: A Generalizable Structure-Based Deep Learning Approach to Drug Discovery	ML scoring function for poses and affinity	Link
07-Jul-24	PUResNetV2.0	PUResNetV2.0: a deep learning model leveraging sparse representation for improved ligand binding site prediction	Predicts ligand binding site on protein surfaces	Link
27-Jun-24	PyAMPA	PyAMPA: a high-throughput prediction and optimization tool for antimicrobial peptides	Discovery and optimization of AMPs	Link
17-Jun-24	PSICHIC	Physicochemical graph neural network for learning protein?ligand interaction fingerprints from sequence data	Protein ligand interaction prediction	Link
17-Jun-24	DeepGlycanSite	Highly accurate carbohydrate-binding site prediction with DeepGlycanSite	Prediction of carbohydrate-binding sites on a protein	Link
10-Apr-24	VN-EGNN	VN-EGNN: E(3)-Equivariant Graph Neural Networks with Virtual Nodes Enhance Protein Binding Site Identification	Pocket identification	Link
13-Feb-24	AMP_ML	Accelerating Antimicrobial Peptide Discovery for WHO Priority Pathogens through Predictive and Interpretable Machine Learning Models	A series of models to predict AMPs and toxicity	Link
04-Jan-24	Prop3D	Prop3D: A flexible, Python-based platform for machine learning with protein structural properties and biophysical data	protein 3D Generate structural data for ML and DL	Link
29-Nov-23	ProteinMAE	ProteinMAE: masked autoencoder for protein surface self-supervised learning	It learns protein surface features to predict binding sites	Link
28-Oct-23	PoseCheck	PoseCheck: Generative Models for 3D Structure-based Drug Design Produce Unrealistic Poses	Benchmark	Link
23-Oct-23	CSM-Potential2	CSM-Potential2: A comprehensive deep learning platform for the analysis of protein interacting interfaces	Prediction of protein interaction interfaces with proteins, nucleic acids, and ligands	Link
22-Dec-22	AlphaPulldown	AlphaPulldown?a python package for protein?protein interaction screens using AlphaFold-Multimer	As the name suggest, it predicts which proteins are likely to interact with a bait protein	Link
07-Nov-22	sAMPpred-GAT	sAMPpred-GAT: prediction of antimicrobial peptide by graph attention network and predicted peptide structure	Predicts the activity & the structure of AMPs	Link
25-Jan-22	Diff-AMP	Diff-AMP: tailored designed antimicrobial peptide framework with all-in-one generation, identification, prediction and optimization	Multi-task to generates, identifies, & optimizes AMPs	Link
20-Jan-21	DeepSurf	A surface-based deep learning approach for the prediction of ligand binding sites on proteins	Predicts ligand binding site on protein surfaces	Link
18-Nov-19	DeepMSA	DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins	Generates multiple sequence alignments	Link