Database |
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PROTAC-DB |
Description: The first web-accessible PROTACs database Link: http://cadd.zju.edu.cn/protacdb/ Citation: Nucleic Acids Research, 2021, 49(D1), D1381-D1387; Nucleic Acids Research, 2023, 51(D1), D1367-D1372 |
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CovalentInDB |
Description: The largest web-accessible resource for covalent inhibitors and related targets Link: http://cadd.zju.edu.cn/cidb/ Citation: Nucleic acids research, 49(D1), D1122–D1129 |
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DDInter |
Description: A comprehensive, professional, and open-access database specific to drug-drug interactions Link: http://ddinter.scbdd.com/ Citation: Nucleic acids research, 2022, 50(D1): D1200-D1207 |
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VGSC |
Description: The largest professional online database of voltage-gated sodium channels Link: http://cadd.zju.edu.cn/vgsc/ Citation: J Cheminformatics, 2022, 14, 75 |
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Molecular featurization |
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BioMedR |
Description: An R/CRAN package for integrated data analysis pipeline in biomedical study Link: https://cran.r-project.org/web/packages/BioMedR/ Citation: Briefings in bioinformatics, 2021, 22(1): 474-484 |
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Scopy |
Description: An integrated negative design Python library for desirable HTS/VS database design Link: https://github.com/kotori-y/Scopy/ Citation: Briefings in Bioinformatics, 2021, 22(3): bbaa194 |
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PySmash |
Description: Python package and individual executable program for representative substructure generation and application Link: https://github.com/kotori-y/pySmash/ Citation: Briefings in Bioinformatics, 2021, 22(5): bbab017 |
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QSAR modeling |
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MGA |
Description: Mining Toxicity Information from Large Amounts of Toxicity Data Link: https://github.com/wzxxxx/MGA/ Citation: Journal of Medicinal Chemistry, 2021, 64(10), 6924-6936 |
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BAN |
Description: Learning to SMILES: BAN-based strategies to improve latent representation learning from molecules Link: https://github.com/zhang-xuan1314/SMILES-BiLSTM-attention-network/ Citation: Briefings in Bioinformatics, 2021, 22(6), bbab327 |
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MG-BERT |
Description: Leveraging unsupervised atomic representation learning for molecular property prediction Link: https://github.com/zhang-xuan1314/Molecular-graph-BERT/ Citation: Briefings in Bioinformatics, 2021, 22(6), bbab152 |
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HRGCN+ |
Description: Hyperbolic relational graph convolution networks plus: a simple but highly efficient QSAR-modeling method Link: https://quantum.tencent.com/hrgcn/ Citation: Briefings in Bioinformatics, 2021, 22(5), bbab112 |
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ADMET prediction |
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OptADMET |
Description: A web-based tool for substructure modifications to improve ADMET properties of lead compounds Link: https://cadd.nscc-tj.cn/deploy/optadmet/ Citation: Nature Protocols, 2024, 19(4), 1105-1121 |
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ADMETlab 3.0 |
Description: An updated comprehensive online ADMET prediction platform enhanced with broader coverage, improved performance, API functionality and decision support Link: https://admetlab3.scbdd.com/ Citation: Nucleic Acids Research, 2024, 52(W1), W422-W431 |
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ADMETlab 2.0 |
Description: An enhanced version of the widely used ADMETlab for systematical evaluation of ADMET properties, as well as some physicochemical properties and medicinal chemistry friendliness Link: https://admetmesh.scbdd.com/ Citation: Nucleic Acids Research, 2021, 49, W5-W14 |
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ChemAGG |
Description: A free web server that could be used to easily filter out aggregators from potential lead molecules Link: https://admet.scbdd.com/ChemAGG/index/ Citation: Journal of Chemical Information and Modeling, 2019, 59(9), 3714-3726 |
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ChemFluo |
Description: A public web server which could be useful to flag blue and green fluorescent compounds in large dataset Link: https://admet.scbdd.com/chemfluo/index/ Citation: Briefings in Bioinformatics, 2021, 22(4), bbaa282 |
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GASA |
Description: A free web server for Graph Attention-based assessment of Synthetic Accessibility (GASA) Link: http://cadd.zju.edu.cn/gasa/ Citation: Journal of Chemical Information and Modeling, 2022, 62(12), 2973-2986 |
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Drug-logS |
Description: A program freely distributed to the public for the estimation of aqueous solubility Link: http://modem.ucsd.edu/adme/ Citation: Journal of chemical information and computer sciences, 2004, 44(1), 266-275 |
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Protein-ligand docking |
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KarmaDock |
Description: A deep learning paradigm for ultra-large library docking with fast speed and high accuracy Link: https://github.com/schrojunzhang/KarmaDock/ Citation: Nature Computational Science, 2023, 3(9), 789-804 |
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CarsiDock |
Description: A deep learning paradigm for accurate protein–ligand docking and screening based on large-scale pre-training Link: https://github.com/carbonsilicon-ai/CarsiDock/ Citation: Chemical Science, 2024, 15(4), 1449-1471 |
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MetalProGNet |
Description: A structure-based deep graph model for metalloprotein-ligand interaction predictions Link: https://github.com/zjujdj/MetalProGNet/ Citation: Chemical Science, 2023, 14(8), 2054-2069 |
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RTMScore |
Description: A protein-ligand scoring function based on residue-atom distance likelihood potential and graph transformer Link: https://github.com/sc8668/RTMScore/ Citation: Journal of Medicinal Chemistry, 2022, 65(15), 10691-10706 |
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IGN |
Description: A deep graph representation learning framework for protein−ligand interaction predictions Link: https://github.com/zjujdj/InteractionGraphNet/tree/master/ Citation: Journal of Medicinal Chemistry, 2021, 64(24), 18209-18232 |
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ML-PLIC |
Description: A web server for the development of customized scoring functions Link: http://cadd.zju.edu.cn/plic/ Citation: Briefings in Bioinformatics, 2023, 24(5), bbad295 |
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Binding free energy prediction |
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CaFE |
Description: A VMD plugin for binding affinity prediction using end-point free energy methods Link: https://github.com/HuiLiuCode/CaFE_Plugin/ Citation: Bioinformatics, 2016, 32(14), 2216-2218 |
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fastDRH |
Description: A web server to predict and analyze protein-ligand complexes based on molecular docking and MM/PB(GB)SA computation Link: http://cadd.zju.edu.cn/fastdrh/overview/ Citation: Briefings in Bioinformatics, 2022, 23(5), bbac201 |
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De novo drug design |
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MCMG |
Description: A multi-constraints molecular generation approach based on conditional transformer and reinforcement learning Link: https://github.com/jkwang93/MCMG/ Citation: Nature Machine Intelligence, 2021, 3(10), 914-922 |
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ChemistGA |
Description: A Chemical Synthesizable Accessible Molecular Generation Algorithm for Real-World Drug Discovery Link: https://github.com/jkwang93/ChemistGA/ Citation: Journal of Medicinal Chemistry, 2022, 65(18), 12482-12496 |
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RELATION |
Description: A Deep Generative Model for Structure-based De Novo Drug Design Link: https://github.com/micahwang/RELATION/ Citation: Journal of Medicinal Chemistry, 2022, 65(13), 9478-9492 |
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Protein-protein docking |
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HawkDock |
Description: A web server for the structural prediction and analysis of protein-protein complex Link: http://cadd.zju.edu.cn/hawkdock/ Citation: Nucleic Acids Research, 2019, 47(W1), W322-W330 |
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Molecular image recognition |
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ABC-Net |
Description: A deep learning architecture for SMILES recognition from molecular images Link: https://github.com/zhang-xuan1314/ABC-Net/ Citation: Briefings in Bioinformatics, 2022, 23(2), bbac033 |
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MICER |
Description: A pre-trained encoder-decoder architecture for molecular image captioning Link: https://github.com/Jiacai-Yi/MICER/ Citation: Bioinformatics, 2022, 38(19), 4562-4572 |
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Drug design tools |
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DrugFlow |
Description: An AI-Driven One-Stop Platform for Innovative Drug Discovery. Link: https://drugflow.com/ Citation: Journal of Chemical Information and Modeling, 2024, 64(14), 5381β5391 |
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KIP |
Description: A web server to predict the inhibitory activity of small molecules against 204 protein kinases simultaneously. Link: http://cadd.zju.edu.cn/kip/ Citation: Acta Pharmaceutica Sinica B, 2023, 13(1), 54-67 |
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farPPI |
Description: A web server for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods Link: http://cadd.zju.edu.cn/farppi/ Citation: Bioinformatics, 2019, 35(10), 1777-1779 |
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ChemTB |
Description: A web server to identify active molecules against mycobacterium tuberculosis through artificial intelligence Link: http://cadd.zju.edu.cn/chemtb/ Citation: Briefings in Bioinformatics, 2021, 22(5), bbab068 |
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DeepChargPredictor |
Description: A web server for predicting QM-based atomic charges via state-of-the-art machine-learning algorithms Link: http://cadd.zju.edu.cn/deepchargepredictor/ Citation: Bioinformatics, 2021, 37(22), 4255-4257 |
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PROTAC-Model |
Description: Integrative modeling of PROTAC-mediated ternary complexes Link: https://github.com/gaoqiweng/PROTAC-Model/ Citation: Journal of Medicinal Chemistry, 2021, 64(21), 16271-16281 |
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