It's an general repository containing multiple script for several task into computational biophysics or biology, which should be update frequently for me.
If you've any questions, please write me to groponp@gmail.com. Programming lenguage used into this repo are: C++, Fortran95, Tcl, Python, Bash, AWK.
If you want get more detail about this script can join to our discord channel: https://discord.gg/ZGpAWtvW
git clone git@github.com:groponp/CompBiology-Biophysics.gitIf you're using any code, please cite our papers:
- Ropón-Palacios et al. (2020) Potential novel inhibitors against emerging zoonotic pathogen Nipah virus: a virtual screening and molecular dynamics approach, Journal of Biomolecular Structure and Dynamics, 38:11, 3225-3234, DOI: 10.1080/07391102.2019.1655480
- Ropón Palacios et al. (2019) Novel multi-epitope protein containing conserved epitopes from different Leishmania species as potential vaccine candidate: Integrated immunoinformatics and molecular dynamics approach, Computational Biology and Chemistry, DOI: https://doi.org/10.1016/j.compbiolchem.2019.107157.
- Otazu et al. (2020) Targeting Receptor Binding Domain and Cryptic Pocket of Spike glycoprotein from SARS-CoV-2 by biomolecular modeling, ARXIV Quantitative Biology, Biomolecules, DOI: https://doi.org/10.48550/arXiv.2006.06452
- Ropón-Palacios e tal. (2022) Glycosylation is key for enhancing drug recognition into spike glycoprotein of SARS-CoV-2, Computational Biology and Chemistry, DOI: https://doi.org/10.1016/j.compbiolchem.2022.107668
- Osorio-Mogollón et al. (2022) Attacking the SARS-CoV-2 Replication Machinery with the Pathogen Box’s Molecules, Letters in Drug Desing & Discovery, DOI: 10.2174/1570180819666220622085659
- Atanda et al. (2023). In silico study revealed the inhibitory activity of selected phytomolecules of C. rotundus against VacA implicated in gastric ulcer, Journal of Biomolecular Structure and Dynamics, DOI: https://doi.org/10.1080/07391102.2022.2160814
It secction given a brief overview of all tools here:
BigBabel.py: It is a script that allows, to convert a large base (> 1 million molecules) of data in 1D-SDF format for PBQT useful to run massive molecular docking.
2_movie_render_fix.tcl: This script generates a video from a molecular dynamics trajectory in full HD, for this you have to have a VMD scene with all the parameters set (amb. occl, light, material, color, representation), that are of your interest.- Co_mol_md.py: This is a simple script, which calculates the number of molecules that can be placed in a simulation box, based on their molar concentration, i.e. Imagine that you want to place 10 mM of Urea in your simulation box, this script will be able to calculate how many molecules you need to place to reach that concentration.
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DeltGtoKd.py/cpp: These two scripts do the same task, use the deltaG value of autodokc4/vina to calculate the dissociation constant (Kd) for a given molecule. In case of the python script it is useful for data < 1 Million , while the one written in C++ is more useful for data > 1 Million. - FEL.py: It is a physical algorithm, which allows the use of two coordinate reactions (commonly RMSD, Rgyr) for a given biological system in order to find its Free Energy lanscape, and determine the sampled metastases. It generate un 2D plot too.
- Getseq.py: This is a script, which allows to obtain all the possible homologous sequences for a given sequence query, and for specific taxa, either to model or perform multiple alignments.
- NAMD2EqStats.py: This is a script that allows to extract the information of pressure, temperature, energy during the equilibration process in molecular dynamics using NAMD.
MakeMSA.R: This is a simple code in R that allows quality alignment and customization, in LaTex format.- MolPack.tcl: It is a long script, which allows to prepare systems in solution (such as protein in water) and systems to perform stretching molecular dynamics.
- OrientZ-axis.py: This script takes a molecule and orients it on the Z axis, for later use, such as in molecular dynamics stretching.
autodock-vina-screening.sh: It is a script that allows you to run virtual screening for a large database, from the conversion of the files to the processing of the results.- contact_map_prot.py: This script allows you to find the number of contacts between two interacting molecules. Mainly between protein-protein.
- convert-namd2charmm.py & convert-namd4gmx.py: These scripts convert the topology and coordinates from NAMD/GRO to charmm. Be careful with this, you might get some errors if the input files are not correct.
- essential-dynamics.sh: This script allows processing molecular dynamics trajectories to obtain the normal modes of motion of a given biomolecule.
- get_box.tcl: This script allows to obtain the dimensions and the docking grid, this allows to use molecules with more than 1M atoms, overcoming the limitation of MGLTools.
- harm-potential-us.py: It is a script that allows estimating the constant k in the bias potential 1/2k(w0-w1), to carry out umbrella sampling.
- jazynski-tclforces.tcl: This is a script based on NAMD's TCLForces, to pull non-equilibrium dynamics.
- make_tclforces.tcl: This script generates the necessary files to be used in TCLForces.
- make_flooding.py: This script allows to generate a flooding system, i.e. a concentration of N ligand in the extracellular part of an aquaporin inserted in a membrane.
- make_segname.tcl: This is a script that allows you to add segname to the PDB files of a given system, to identify parts of a system, to facilitate analysis.
- *mda_2Dmatrix_fix.py: This generates a 2D matrix of the conformational arrangement of a biomolecule.
- mda_convert-traj_fix.py: It interconverts NAMD/GROMACS path files.
- mda_(rgyr,rmsd,rmsf)_fix.py: These scripts perform Rgyr, RMSD, RMSF analysis on a NAMD/GROMACS trajectory.
- molywood_movie.tcl: This is a script based on the molywood library, which allows you to customize videos from simulation data in a more intuitive way.
- prepare_charmm_gui-inputs.py: This generates input fix for use in charmm-gui, mainly for preparing protein-ligand systems.
- remove-PBC-effects.py: This script removes the effects of PBC in a dynamic and makes further analysis suitable.
- remove_rot+trans.py: This script removes the rotation and translation movements to smooth the molecular dynamics trajectory and be able to visualize it without jump effects.
- running_analysis.sh: This is a meta-script that gives an example of running different scripts in python or another language in bash, to automate analysis on big data.
- sf2pdb_script.sh: This script uses openbabel to convert files from SDF to PDB.
- vitscreen_script.sh: This script uses autodockvina to run a virtual screening.
- vmd_merge_pdb_fix.tcl: This script merges multiple pdb files into a single file using the TopoTools library.
- vmd_reducetraj_fix.tcl: This script allows reducing the size of the trajectories of the molecular dynamics simulation, to have a better handling of them, on a workstation with little computational power.
- vmd_rmsd_to_beta_fix.tcl: This script adds the average RMSD values for the beta column of the PDB file and allows coloring based on this value.
- vmd_sasa_fix.py: This script allows to calculate the SASA value for a given selection.
- vmd_segid_to_chain_fix.tcl: This script adds the string name for a PBD from the SEGID.
- RunHPCMD.sh: This is a long script that allows you to run NAMD/GROMACS molecular dynamics in a segmented manner. Example: Imagine that you have to run 100 ns of simulation, but you are running it on an HPC, which sets limited usage times per job (5 days maximum), and you cannot estimate the performance, so send the 100 ns in 5 days, it could result in an error, since it could not be completed, this script divides the simulation into discrete times and automatically resends them, until the entire simulation is completed.
- make_gmx_atom_index.py: It is a simple script, which allows to create atom index to gromacs, with a very simple selection, which is very similar to VMD, but based on MDAnalysis. For example in gromacs it is very difficult to create an index to restrict atoms to within 5 A of a given atom, but here this can be done in a simple way, "name CA around 5 of rename LIG", for example.
Icons in this repo were taken from flaticon