Tutorials of MolAICal V1.3
Notice: All the tutorials Instructions and materials are in Github. If Github is unable for downloading related tutorial files, all the files can be downloaded from Onedrive: All_files or from Gitlab: All_files_InChina.
Quick start 1: Trying MolAICal for molecular docking quickly by clicking "pdf file", materials: files
Quick start 2: Trying MolAICal for molecular growth quickly by clicking "HTML URL", materials: files
1. Drug design tutorials of MolAICal
1.1. Tutorials of 3D drug design by AI and de novo method. The glucagon receptor (GCGR) is selected as an example target. Instructions: pdf file, materials: files
1.2. Tutorials of 3D drug design by AI and virtual screening method. The SARS-CoV-2 Mpro is selected as an example target. Instructions: pdf file, materials: files
1.3. Tutorials of classical virtual screening. Two steps for virtual screening in the pocket of SARS-CoV-2 Mpro. Instructions: pdf file, materials: files
1.4. MM/GBSA tutorial by NAMD and MolAICal. This tutorial is based on the results of molecular dynamics (MD) simulations of SARS-CoV-2 Mpro. Decomposing the free energy contributions to the binding free energy of residues and entropy calculation are also contained in this tutorial. Instructions: pdf file, materials: files
2. Useful drug design tools of MolAICal
2.1. Tutorials of the hole, pore or channel radii calculation of protein or nanotube by MolAICal. Instructions: pdf file, materials: files
2.2. Tutorial of the simple regression model of QSAR for drugs by MolAICal. Instructions: pdf file, materials: files
2.3. Tutorial of potential of mean force (PMF) for energy landscape based on the results of molecular dynamics simulations by MolAICal. Instructions: pdf file, materials: files
2.4. Tutorial of assessing vinardo score of ligands based on the grid file of SARS-CoV-2 Mpro by MolAICal. Instructions: pdf files, materials: files
2.5. Tutorials of the calculations of Synthetic Accessibility, Lipinski's rule of five and Pan-assay interference compounds (PAINS) by MolAICal. Instructions: pdf file, materials: files
2.6. Tutorial of binding free energy based on the value of Kd, Ki, pKd or pKi by MolAICal. Instructions: pdf file, materials: files
2.7. Tutorial of ligand similarity search or comparison based on the fingerprint similarity and 3D structural similarity. Instructions: pdf file, materials: files
2.8. Tutorial of splitting ligands into smaller pieces by MolAICal. Instructions: pdf file, materials: files
3. Tutorial of artificial intelligence by MolAICal
3.1. Tutorials of binding affinity calculation between proteins and ligands by MolAICal and OnionNet model. Instructions: pdf file, materials: files
3.2. Tutorials of binding affinity calculation between proteins and ligands by MolAICal and Pafnucy model. Instructions: pdf file, materials: files
3.3. Tutorials of molecular generation and drug modification by MolAICal and webserver. Instructions: pdf file, materials: files
4. Specialized topics of MolAICal
4.1. Cluster virtual screening results based on binding score and 3D structural similarity. Instructions: pdf file, materials: files
5. Tutorials of development version of MolAICal
Notice: tutorials on this part are only for the development version of MolAICal. If the official release of MolAICal is available based on the previous development version. The below tutorials will be moved above, and please find the related tutorials in the above parts.
5.1. Tutorials of the predictions of drugs ADMET (absorption, distribution, metabolism, excretion, and toxicity) and molecular properties. Download instruction pdf file named "ADMETProCalculationTutorial.pdf": pdf file, materials: files
5.2. Tutorial on batch format conversion of receptors and ligands, and continuing run of virtual screening by MolAICal. Download instruction pdf file named "convert_rec_lig_batch_tutorial.pdf": pdf file, materials: files