jianlin-cheng

CryoTransformer

A transformer model for picking protein particles in cryo-EM images

DeepGRN

Deep learning for modeling gene regulatory network

TransFun

Transformer for protein function prediction

CATA

Collaborative Attentive-Autoencoder for scientific article recommendation

CryoSegNet

Customized foundational image segmentation models for picking protein particles in cryo-EM images

DRLComplex

Deep reinforcement learning for protein complex modeling

DeepComplex

Deep learning prediction of inter-chain contacts of protein complex

DProQA

GNET2

Gene regulatory network modeling tool (GNET2)

PreMut

Accurate prediction of single-site mutation induced changes on protein structures with equivariant graph neural networks

DRCon

Deep dilated convolutional residual neural network for predicting interchain contacts of protein homodimers

PRO3DCNN

3D Convolutional Neural Networks for Classifying Protein Structures into Folds

DeepComplex2

Deep learning prediction of protein complex structures from sequences

DeepProLigand

A deep learning bioinformatics pipeline for protein-ligand complex structure prediction

DISTEMA

Prediction of the quality of single protein model using deep learning and residue-residue distance maps

InterpretContactMap

Deep learning methods for interpreting protein contact maps

MULTICOM_Human_CASP14

MULTICOM human system for CASP14 tertiary structure prediction

DeepCryoEM

Deep learning methods for CryoEM data analysis

DistDom

Deep learning prediction of protein domains from distance maps

DNCON2_Inter

Predicting inter-protein contacts using DNCON2

SAXSDom

This is a bioinformatics tool to use SAXS data to assemble protein domain structures into full-length structural models

BML_FAQ

This repository contains the frequently asked questions, their answers and the description of resources in the Bioinformatics and Machine Learning Lab (BML).

Cryo2Struct

Deep learning tools for converting cryo-EM density maps to protein structures

DFOLD

The distance-based protein folding

DeepCryoTrace

Deep learning methods to predict protein backbone trace from cryoEM images

DeepRank

The deep learning method for ranking protein structural models

DeepRank3

Deep learning prediction of the quality of protein structural models with inter-residue distance maps

DRCon_Hetero

Deep learning method for predicting interchain contacts in heterodimers

GFOLD

Distance-based protein folding based on gradient descent optimization

ProBST

Protein binding site prediction with transformers