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| name: unittests | ||
| name: ci | ||
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| on: push | ||
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| jobs: | ||
| build: | ||
| test: | ||
| runs-on: ubuntu-latest | ||
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| steps: | ||
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| ## Uncomment a line if you want to skip a given category of checks | ||
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| #skip_repository_checks_reason: <reason for skipping goes here> | ||
| #skip_license_checks_reason: <reason for skipping goes here> | ||
| #skip_registry_checks_reason: <reason for skipping goes here> | ||
| #skip_citation_checks_reason: <reason for skipping goes here> | ||
| skip_checklist_checks_reason: "I'm using the Codacy dashboard to guide my development" | ||
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| ignore_commented_badges: false |
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| # PRODIGY-LIG / Small Molecule Binding Affinity Prediction | ||
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| [](https://github.com/haddocking/prodigy-lig/actions/workflows/unittests.yml) | ||
| [](https://www.codacy.com/gh/haddocking/prodigy-lig/dashboard?utm_source=github.com&utm_medium=referral&utm_content=haddocking/prodigy-lig&utm_campaign=Badge_Grade) | ||
| [](https://www.codacy.com/gh/haddocking/prodigy-lig/dashboard?utm_source=github.com&utm_medium=referral&utm_content=haddocking/prodigy-lig&utm_campaign=Badge_Coverage) | ||
| [](https://fair-software.eu) | ||
| [](https://zenodo.org/badge/latestdoi/118625187) | ||
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| Table of Contents | ||
| ================= | ||
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| * [Introduction](#introduction) | ||
| * [Installation](#installation) | ||
| * [Quick start](#quick-start) | ||
| * [Usage](#usage) | ||
| * [Command line arguments](#command-line-arguments) | ||
| * [Required arguments](#required-arguments) | ||
| * [Input file](#input-file) | ||
| * [Chain specification](#chain-specification) | ||
| * [Optional arguments](#optional-arguments) | ||
| * [Electrostatics Energy](#electrostatics-energy) | ||
| * [Distance cutoff](#distance-cutoff) | ||
| * [Processed output file](#processed-output-file) | ||
| * [Verbosity](#verbosity) | ||
| * [Version](#version) | ||
| * [I don't like the command line.](#i-dont-like-the-command-line) | ||
| * [Licensing](#licensing) | ||
| * [Citing us](#citing-us) | ||
| * [Contact](#contact) | ||
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| # Introduction | ||
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| PRODIGY-LIG (PROtein binDIng enerGY prediction - LIGands) is a structure-based | ||
| method for the prediction of binding affinity in protein-small ligand (such as | ||
| drugs or metabolites) complexes. | ||
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| Here is reported a collection of scripts what you can download and use to predict | ||
| the binding addinity of your complex. | ||
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| If you are not familiar with scripting, the online version | ||
| of PRODIGY-LIG can be found here: | ||
| * [PRODIGY-LIG](https://nestor.science.uu.nl/prodigy/lig) | ||
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| # Installation | ||
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| prodigy_lig is [python 3](https://www.python.org/) code and it depends on | ||
| [biopython](http://biopython.org/). | ||
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| From the command line terminal run the following command: | ||
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| ```sh | ||
| pip install git+https://github.com/haddocking/prodigy-lig | ||
| ``` | ||
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| If you are installing to a system-wide location (e.g. `/usr/bin`) you might | ||
| need elevated privileges. | ||
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| `prodigy_lig` should now be accessible from the command line. | ||
| PRODIGY-LIG (**PRO**tein bin**DI**ng ener**GY** prediction - **LIG**ands) is a structure-based method for the prediction of binding affinity in protein-small ligand (such as drugs or metabolites) complexes. | ||
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| # Quick start | ||
| It's also available as a web service @ [wenmr.science.uu.nl/prodigy-lig](https://wenmr.science.uu.nl/prodigy-lig) | ||
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| You can fetch a structure from the PDB and start using the code immediately. | ||
| The following two lines should do the trick: | ||
| ## Installation | ||
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| ```text | ||
| pip install prodigy-lig | ||
| ``` | ||
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| ## TL:DR | ||
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| You can fetch a structure from the PDB and start using the code immediately. The following two lines should do the trick: | ||
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| ```text | ||
| wget https://files.rcsb.org/download/1A0Q.pdb | ||
| prodigy_lig.py -c H,L H:HEP -i 1A0Q.pdb | ||
| ``` | ||
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| If all goes well this will produce the following two lines of output. | ||
| ```text | ||
| $ prodigy_lig -c H,L H:HEP -i 1A0Q.pdb | ||
| ``` | ||
| Job name DGprediction (low refinement) (Kcal/mol) | ||
| 1a0q -8.49 | ||
| ``` | ||
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| You can read more about the usage of prodigy_lig in the next section | ||
| You can read more about the usage of `prodigy_lig` in the next section | ||
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| # Usage | ||
| ## Usage | ||
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| Running `prodigy_lig -h` will list some basic information about the code. | ||
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| ``` | ||
| ```text | ||
| usage: prodigy_lig [-h] -c CHAINS CHAINS -i INPUT_FILE [-e ELECTROSTATICS] | ||
| [-d DISTANCE_CUTOFF] [-o] [-v] [-V] | ||
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@@ -129,159 +87,100 @@ Authors: Panagiotis Koukos, Anna Vangone, Joerg Schaarschmidt | |
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| For all the examples mentioned below the following two caveats apply: | ||
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| **prodigy_lig only considers contacts between the ligand and residues of the | ||
| protein**. Any cofactors, ions or solvent molecules that might be present, | ||
| are not included in the distances that are calculated. | ||
| > **prodigy_lig only considers contacts between the ligand and residues of the protein**. Any cofactors, ions or solvent molecules that might be present, are not included in the distances that are calculated. | ||
| Additionaly, prodigy_lig **only works on single model structures**. That means | ||
| that if your structure of interest contains multiple models (e.g. NMR conformers) | ||
| only the first model will be used for the calculations. | ||
| Additionaly, prodigy_lig **only works on single model structures**. That means that if your structure of interest contains multiple models (e.g. NMR conformers) only the first model will be used for the calculations. | ||
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| ## Command line arguments | ||
| ### Command line arguments | ||
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| The command line arguments belong to one of two categories; required and optional. | ||
| The two required arguments are the input structure file and the specification of | ||
| the chain and residue identifiers of the interactors. | ||
| The command line arguments belong to one of two categories; required and optional. The two required arguments are the input structure file and the specification of the chain and residue identifiers of the interactors. | ||
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| ### Required arguments | ||
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| #### Input file | ||
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| The input structure file can be specified with the `-i` flag (or `--input_file`) | ||
| and it should be the path to the input PDB/mmCIF file. | ||
| The input structure file can be specified with the `-i` flag (or `--input_file`) and it should be the path to the input PDB/mmCIF file. | ||
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| #### Chain specification | ||
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| The `-c` flag (or `--chains`) must be used to specify the chain identifiers for | ||
| the interactors, and for the ligand the residue identifier as well. The first | ||
| argument allows to specify the protein chains to be used in the analysis. Multiple | ||
| chains can be specified by comma separating them. The second argument needs to | ||
| specify the chain and residue identifier of the ligand of interest separated by | ||
| a colon (`:`). | ||
| The `-c` flag (or `--chains`) must be used to specify the chain identifiers for the interactors, and for the ligand the residue identifier as well. The first argument allows to specify the protein chains to be used in the analysis. Multiple chains can be specified by comma separating them. The second argument needs to specify the chain and residue identifier of the ligand of interest separated by a colon (`:`). | ||
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| For the next examples we will be using the structure from the quickstart | ||
| [section](#quick-start), 1A0Q. | ||
| For the next examples we will be using the structure from the quickstart, 1A0Q. | ||
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| If you didn't do so before you can fetch the PDB file with the following line of | ||
| code from the command line. | ||
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| ``` | ||
| ```text | ||
| wget https://files.rcsb.org/download/1A0Q.pdb | ||
| ``` | ||
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| Or by simply pointing your browser [here](https://files.rcsb.org/download/1A0Q.pdb) | ||
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| After examining the file with your favourite molecular viewer you will note that | ||
| this is a Fab fragment with a small molecule ligand embedded between the heavy and | ||
| light chains. The chain identifiers of the heavy and light chains are H and L, and | ||
| the small molecule of interest has the residue identifier `HEP` and is part of chain | ||
| H. | ||
| After examining the file with your favourite molecular viewer you will note that this is a Fab fragment with a small molecule ligand embedded between the heavy and light chains. The chain identifiers of the heavy and light chains are H and L, and the small molecule of interest has the residue identifier `HEP` and is part of chain H. | ||
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| The simplest analysis we can do is to include both chains | ||
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| ``` | ||
| ```text | ||
| prodigy_lig -c H,L H:HEP -i 1A0Q.pdb | ||
| ``` | ||
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| which produces the following output. | ||
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| ``` | ||
| ```text | ||
| Job name DGprediction (low refinement) (Kcal/mol) | ||
| 1a0q -8.49 | ||
| ``` | ||
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| In this case, atomic distances from the ligand to residues of both chains have | ||
| been calculated. | ||
| In this case, atomic distances from the ligand to residues of both chains have been calculated. | ||
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| If we wanted to only include the heavy chain (`H`) in the analysis we would use | ||
| this command instead. | ||
| If we wanted to only include the heavy chain (`H`) in the analysis we would use this command instead. | ||
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| ``` | ||
| ```text | ||
| prodigy_lig -c H H:HEP -i 1A0Q.pdb | ||
| ``` | ||
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| which would produce this output | ||
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| ``` | ||
| ```text | ||
| Job name DGprediction (low refinement) (Kcal/mol) | ||
| 1a0q -6.69 | ||
| ``` | ||
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| ### Optional arguments | ||
| #### Optional arguments | ||
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| The first two optional arguments will affect your results, whereas the latter ones | ||
| will only impact the formatting and content of your output. | ||
| The first two optional arguments will affect your results, whereas the latter ones will only impact the formatting and content of your output. | ||
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| #### Electrostatics Energy | ||
| ##### Electrostatics Energy | ||
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| In addition to the contact information prodigy_lig can make use of the electrostatic | ||
| energy of the interaction as well. This refers to the intermolecular electrostatic | ||
| energy as calculated by [HADDOCK](https://wenmr.science.uu.nl/haddock2.4). | ||
| In addition to the contact information prodigy_lig can make use of the electrostatic energy of the interaction as well. This refers to the intermolecular electrostatic energy as calculated by [HADDOCK](https://wenmr.science.uu.nl/haddock2.4). | ||
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| If you know this energy because you have refined your complex through HADDOCK then | ||
| you can specify this using the `-e` flag (`--electrostatics`). Additionaly, if your | ||
| PDB file is coming from HADDOCK, `prodigy_lig` will automatically extract the relevant | ||
| information from the input file and make use of it. | ||
| If you know this energy because you have refined your complex through HADDOCK then you can specify this using the `-e` flag (`--electrostatics`). Additionaly, if your PDB file is coming from HADDOCK, `prodigy_lig` will automatically extract the relevant information from the input file and make use of it. | ||
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| #### Distance cutoff | ||
| ##### Distance cutoff | ||
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| This is the cutoff used when calculating the atomic contacts. By default it has a | ||
| value of 10.5 Angstrom, which was identified when training the model. You can modify | ||
| this with the `-d` flag (`--distance_cutoff`). | ||
| This is the cutoff used when calculating the atomic contacts. By default it has a value of 10.5 Angstrom, which was identified when training the model. You can modify this with the `-d` flag (`--distance_cutoff`). | ||
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| #### Processed output file | ||
| ##### Processed output file | ||
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| If you would like a copy of the structure that was used to calculate the atomic | ||
| contacts you can use the `-o` flag (`--output_file`). This might be useful if you | ||
| have chosen to exclude some chains from the analysis. The file will be created in | ||
| the current working directory and its filename will be `input_name-processed.pdb`. | ||
| If you would like a copy of the structure that was used to calculate the atomic contacts you can use the `-o` flag (`--output_file`). This might be useful if you have chosen to exclude some chains from the analysis. The file will be created in the current working directory and its filename will be `input_name-processed.pdb`. | ||
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| #### Verbosity | ||
| ##### Verbosity | ||
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| If you specify the `-v` flag (`--verbose`), in addition to the DG values / scores, | ||
| the output will include the contact counts and, if defined, electrostatics as well. | ||
| Once again using the same example as above. | ||
| If you specify the `-v` flag (`--verbose`), in addition to the DG values / scores, the output will include the contact counts and, if defined, electrostatics as well. Once again using the same example as above. | ||
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| ``` | ||
| ```text | ||
| prodigy_lig -c H,L H:HEP -i 1A0Q.pdb -v | ||
| ``` | ||
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| Will produce the following output | ||
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| | Job name | DGprediction (low refinement) (Kcal/mol) | CC | CN | CO | CX | NN | NO | NX | OO | OX | XX | ||
| | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | | ||
| | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ||
| | 1A0Q | -8.49 | 1838 | 589 | 1010 | 124 | 27 | 175 | 30 | 132 | 24 | 0 | ||
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| #### Version | ||
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| Finally you can use the `-V` flag (`--version`) to get the version of the code. | ||
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| ## I don't like the command line. | ||
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| Too bad. Luckily for you, prodigy_lig has also been implemented in a freely accessible | ||
| [webserver](https://bianca.science.uu.nl/prodigy/lig). | ||
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| # Licensing | ||
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| prodigy_lig is licensed under [Apache 2.0](LICENSE). | ||
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| # Citing us | ||
| ## Citing us | ||
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| If our predictive model or any scripts are useful to you, consider citing them in your | ||
| publications: | ||
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| **Vangone A, Schaarschmidt J, Koukos P, Geng C, Citro N, Trellet M, Xue L, Bonvin A.**: Large-scale | ||
| prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server. *Bioinformatics*, | ||
| ([link](https://doi.org/10.1093/bioinformatics/bty816)) | ||
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| **Kurkcuoglu Z, Koukos P, Citro N, Trellet M, Rodrigues J, Moreira I, Roel-Touris J, | ||
| Melquiond A, Geng C, Schaarschmidt J, Xue L, Vangone A, Bonvin AMJJ.**: Performance | ||
| of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in | ||
| the D3R Grand Challenge 2. *J Comput Aided Mol Des* 32(1):175-185 (2017). ([link](https://link.springer.com/article/10.1007/s10822-017-0049-y)) | ||
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| # Contact | ||
| - **Vangone A, Schaarschmidt J, Koukos P, Geng C, Citro N, Trellet M, Xue L, Bonvin A.**: [Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server.](https://doi.org/10.1093/bioinformatics/bty816) *Bioinformatics* | ||
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| Issues? Bug reports? Suggestions? Feel free to | ||
| [submit](https://github.com/haddocking/prodigy-lig/issues) an issue. Alternatively, | ||
| you can reach us at [email protected]. | ||
| - **Kurkcuoglu Z, Koukos P, Citro N, Trellet M, Rodrigues J, Moreira I, Roel-Touris J, Melquiond A, Geng C, Schaarschmidt J, Xue L, Vangone A, Bonvin AMJJ.**: [Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2](https://link.springer.com/article/10.1007/s10822-017-0049-y). *J Comput Aided Mol Des* 32(1):175-185 (2017). | ||
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