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Ligands

Databases & Tools for PROTAC and Protein Research

Databases

PROTAC-DB 3.0

Manually curated database for PROTAC molecules with degradation capacity, binding affinities and cellular activities.

RCSB PDB

Archieve of 3D structures of large biomolecules (Proteins,DNA,RNA) and their complexes.

PROTACpedia

Manually curated collaborative and comprehensive resource for POroteolysis targeting chimeras (PROTACs).

PDBbind+

Comprehensive collection of experimental Binding affinity data for biomolecules recorded in RCSB PDB.

AlphaFold DB

Collection of over 200 million predicted protein structures using AlphaFold.

BindingDB

Binding affinity database focusing on protein complexes considered as drug targets.

PubChem

Open chemistry database for small and large molecules.

ZINC15

A free database of commercially available compounds for virtual screening.

DrugBank

Comprehensive database of approved & experimental drugs.

Tools

DeepPROTACs

A deep neural network model that predicts degradation capacity of PROTAC molecule based on structure of given target protein and E3 ligase.

DiffPROTACs

Transformers based model that learns and generates new PROTAC linkers based on given ligands.

SwissADME

Website that allows to compute physicochemical descriptors and predict ADME parameters, pharmacokinetic properties, druglike nature and medicinal chemistry friendliness of small molecules.

PlayMolecule

A virtual environment for drug discovery where simulation, AI and data are integrated.

ChemProp

A machine learning package for chemical property prediction using D-MPNN architecture.

DeepChem

Open-source ML toolchain that democratizes the use of Deep-learning in drug discovery, material science, quantum chemistry and biology.

ProteinPlus

A webserver for structure-based molecular modeling. provides functionalities for structure quality assessment, hydrogen placement, search alternative conformations.

PROTAC-design-evaluator (PRODE)

A novel in-silico methodology for PROTAC designing