{"id":15637870,"url":"https://github.com/rasbt/protein-science","last_synced_at":"2025-10-29T13:38:34.194Z","repository":{"id":13721367,"uuid":"16415516","full_name":"rasbt/protein-science","owner":"rasbt","description":"A collection of useful tutorials for Protein Science","archived":false,"fork":false,"pushed_at":"2015-06-29T17:22:25.000Z","size":15640,"stargazers_count":105,"open_issues_count":0,"forks_count":41,"subscribers_count":13,"default_branch":"master","last_synced_at":"2025-03-30T13:23:17.459Z","etag":null,"topics":["protein-data-bank","protein-science","python"],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/rasbt.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2014-01-31T17:49:29.000Z","updated_at":"2025-02-28T09:14:50.000Z","dependencies_parsed_at":"2022-09-06T00:20:44.921Z","dependency_job_id":null,"html_url":"https://github.com/rasbt/protein-science","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rasbt%2Fprotein-science","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rasbt%2Fprotein-science/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rasbt%2Fprotein-science/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rasbt%2Fprotein-science/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/rasbt","download_url":"https://codeload.github.com/rasbt/protein-science/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":251652200,"owners_count":21621902,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["protein-data-bank","protein-science","python"],"created_at":"2024-10-03T11:13:56.014Z","updated_at":"2025-10-29T13:38:29.155Z","avatar_url":"https://github.com/rasbt.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n\n#### About this repository\n[[back to top](#about-this-repository)]\n\nDuring my work and hobbies, I started accumulating useful material about different topics in Protein-Science, which I wanted to collect in a central place and share with others in hope that it might serve as a useful reference one day.\n\n\u003cbr\u003e\n\u003cbr\u003e\n\n- [Software Quick Guides](./scripts-and-tools/more_protein-science_tools.md)\n- [Tutorials](#tutorials)\n    - [Substructure Alignment Using OpenEye OEChem RMSD](#substructure-alignment-using-openeye-oechem-rmsd)\n    - [Low-Energy Conformer Generation and Overlay](#low-energy-conformer-generation-and-overlay)\n\t- [Molecular docking, estimating free energies of binding, and AutoDock's semi-empirical force field](#molecular-docking-estimating-free-energies-of-binding-and-autodocks-semi-empirical-force-field)\n\n- [Scripts and Tools](#scripts-and-tools)\n- [Info Sheets](#info-sheets)\n- [Literature](#literature)\n- [Protein Science Glossary](#protein-science-glossary)\n- [Useful Links](#useful-links)\n\n\n\u003cbr\u003e\n\u003cbr\u003e\n\n#### I am looking forward to your contributions, suggestions, and ideas\n[[back to top](#about-this-repository)]\n\nIf you have any suggestions or want to make additions, I would be very happy if you could send me  \n\n- an [email](mailto:se.raschka@gmail.com),  \n- leave me a message on [google+](https://plus.google.com/118404394130788869227/),   \n- or even send me a tweet on [twitter](https://twitter.com/rasbt) (given you can fit it within the 140 character limit ;)).  \n\nOr even better: It would be great if you would simply fork this project and send me a pull request.\n\n\u003cbr\u003e\n\u003cbr\u003e\n\u003cbr\u003e\n\u003cbr\u003e\n\n# Tutorials\n[[back to top](#about-this-repository)]\n\n\n\n### Substructure Alignment Using OpenEye OEChem RMSD\n[[back to top](#about-this-repository)]\n\n![steroid substructure](./tutorials/substructure_alignment/Images/reference_substructure.png)\n\nA how-to for extracting a substructure from a molecule and use it as query for an alignment to target molecules.  \n[Link to tutorial](./tutorials/substructure_alignment/README.md)\n\n\u003cbr\u003e\n\n### Low-Energy Conformer Generation and Overlay\n[[back to top](#about-this-repository)]\n\n![low-energy overlay](./tutorials/low_energy_conformer_overlay/Images/ZINC_00062008_confs_2_small.png)\n\nTutorial and script to generate low-energy conformers of query and target molecules and overlay them to choose the highest-scoring hit using OpenEye software.  \n[Link to tutorial](./tutorials/low_energy_conformer_overlay/README.md)\n\n\u003cbr\u003e\n\n### Molecular docking, estimating free energies of binding, and AutoDock's semi-empirical force field\n\n[[back to top](#about-this-repository)]\n\n![](./tutorials/scoring_functions_and_autodock/Images/prot_lig_complexes.png)\n\nDiscussions and questions about methods, approaches, and tools for estimating (relative) free binding energies of protein-ligand complexes are quite popular, and even the simplest tools can be quite tricky to use. Here, I want to briefly summarize the idea of molecular docking, and give a short overview about how we can use AutoDock 4.2's hybrid approach for evaluating binding affinities.  \n\n[Link to tutorial](./tutorials/scoring_functions_and_autodock/2014_autodock_energycomps.md)\n\n\u003cbr\u003e\n\u003cbr\u003e\n\u003cbr\u003e\n\n\n\u003chr\u003e\n\n\n# Scripts and Tools\n[[back to top](#about-this-repository)]\n\n- A useful [one-liner cheatsheet](./scripts-and-tools/oneliner.md) for quick and simple commands for working with protein structure files.\n\n- the **[`scripts-and-tools`](./scripts-and-tools)** subdirectory with tools for, e.g., \n\t- [`center_of_mass.py`](./scripts-and-tools/center_of_mass) - calculating the center of mass of protein and ligands \n\t- [`pdb_to_fasta.py`](./scripts-and-tools/pdb_to_fasta) - converting PDB files into FASTA strings\n\t- [`rmsd.py`](./scripts-and-tools/rmsd) - calculating the RMSD between two molecules\n\t- [`grab_atom_radius.py`](./scripts-and-tools/grab_atom_radius) - extracting coordinates from PDB files \n\t- [`renumber_pdb.py`](./scripts-and-tools/renumber_pdb) - renumbering atoms and residues in PDB files\n\t- [`split_multimol2.py`](./scripts-and-tools/split_multimol2) - splitting a multi-MOL2 file into individual MOL2 files\n\t- [`strip_h.py`](./scripts-and-tools/strip_h) - stripping Hydrogen atoms for single PDB files or nested directories of PDB files\n\n\n- **[smilite](https://github.com/rasbt/smilite)** - a Python module to download and analyze SMILE strings (Simplified Molecular-Input Line-entry System) of chemical compounds from ZINC\n\n- **[pyprot](https://github.com/rasbt/pyprot)** - a Python package for working with protein structure files formats. It comes with a collection of ready-to-use scripts for the most common file operations and protein analyses.\n\n\n- **[PDB Info Table](https://github.com/rasbt/datacollect/tree/master/pdb_infotable)** - A simple command line tool that creates an info table from a list of PDB files.\n\n\u003cbr\u003e\n\u003cbr\u003e\n\u003cbr\u003e\n\n\u003chr\u003e\n\n\n# Info Sheets\n[[back to top](#about-this-repository)]\n\n- Iridium dataset of high-quality protein structures [PDB code quickreference](./info_sheets/Iridium_pdb_codes.md)\n\n\u003cbr\u003e\n\u003cbr\u003e\n\n\u003chr\u003e\n\n\n# Literature\n\n[[back to top](#about-this-repository)]\n\n- [Literature overview and summaries](./literature/literature_summaries.md)\n\n\n\n\u003cbr\u003e\n\u003cbr\u003e\n\n\u003chr\u003e\n\n\n# [Protein Science Glossary](./glossary/README.md)\n[[back to top](#about-this-repository)]\n\n\u003cbr\u003e\n\u003cbr\u003e\n\n\u003chr\u003e\n\n\n# Useful Links\n[[back to top](#about-this-repository)]\n\n- [ZINC](http://zinc.docking.org)  \n A free database for \u003e 35 million purchasable chemical compounds for virtual screening.\n \n- [RCSB Protein Data Bank (PDB)](http://www.rcsb.org)  \nThe world's largest repository for downloadable 3D structures of biological molecules, including protein nucleic acid (DNA) structures.\n\n- [EMBL-EBI PDBsum](http://www.ebi.ac.uk/pdbsum/)  \nA Pictorial database of 3D structures in the Protein Data Bank that provides additional useful information, e.g., visualization between protein-ligand interactions.\n\n- [Ligscore - Pose \u0026 Rank](http://modbase.compbio.ucsf.edu/ligscore/)  \nA web server for scoring protein-ligand complexes based on statistical potentials.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frasbt%2Fprotein-science","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frasbt%2Fprotein-science","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frasbt%2Fprotein-science/lists"}