Prodigy: 'Son'

Description: Prediction of the binding affinity (∆G) of several docked structures using prodigy software.
Language: bash script.
Operating system: Linux.
Prodigy link: Here
Code link: Here

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Gromacs: 'Haaland'

Description: Running molecular dynamics simulations and numerous Post MD analysis for several pdb files using GROMACS software.
Language: Linux.
Operating system: Linux.
Gromacs link: Here
Code link: Here

Assembly code: 'Henry'

Description: This code assembles the basic parts of our library to create every possible probability of protease switches with your own collection of inhibitors, linkers, and peptides.
Language: Python.
Operating system: Any operating system.
Code link: Here

QA: 'Modric'

Description: Extracts JSON files of assisted 3D models from the Swiss Model Structure Assessment server to rank them according to generated parameters.
Language: bash script.
Operating system: Linux.
Swiss Structure Assesment link: Here
Code link: Here

Lightdock: 'MoSalah'

Description: MoSalah code is our optimized code to run flexible docking for a set of receptors against a set of ligands in a matrix-based manner using lightdock software.
Language: bash script.
Operating system: Linux.
Lightdock link: Here
Code link: Here

JSON Ranking of QA output: 'Abu Trika.'

Description: Ranking of models retrieved from Swiss Structure Assessment Server according to parameters of the Quality Assessment code: C-beta deviations, clash score, Molprobity, Ramachandran favored, Ramachandran outliers, Qmean 4, and Qmean 6.
Language: Python.
Operating system: Windows and Linux.
Code link: Here

Enzyme Activity (Michaelis-Menten kinetics): 'Maldini.'

Description: This code measures the velocity of a reaction that is activated by an enzyme over substrate concentration.
Language: MATLAB.
Operating system: Windows.
Code link: Here

Transcription and translation code: 'Buffon.'

Description: This code measures the concentration of mRNA and protein under IPTG induction using an ODE model to simulate the whole process.
Language: Python.
Operating system: Any operating system.
Code link: Here

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Ubiquitin-Proteasome system simulator: ‘Van dijk’

Description: Simulates the whole process of Ubiquitin-Proteasome cascade and predict the rate of substrate degradation.
Language: Python.
Operating system: Windows or Linux.
Code link: Here