A Python Package for the Localization of Protein Modifications in Mass Spectrometry Data by Anthony S. Barente (14035175)

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Average quality scores of the models of the analysis set as a function of the <i>w</i>_<i>SP</i> with which the DOPE potential has been included in the objective function... by Giacomo Janson (8138517)

3D modeling qualities of the AS single-template models built by including DOPE in the objective function of MODELLER. by Giacomo Janson (8138517)

3D modeling qualities of the AM multiple-template models built by including DOPE in the objective function of MODELLER. by Giacomo Janson (8138517)

Modular architecture design of PyNoetic showing all its constituent functions. by Gursimran Singh (575288)

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Adaptive H-REMD simulation algorithm. by Danial Pourjafar-Dehkordi (7165523)

Overview of functionality supported by PyNoetic and its various modules, including the live analysis and programmable flowchart. by Gursimran Singh (575288)

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Listed python codes of our algorithm with explanations (Python 3.9 recommended). by Takayuki Niizato (162226)

The proposed method for protein function prediction. by Seyyede Fatemeh Seyyedsalehi (10196767)

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Explained variance ration of the PCA algorithm. by Abeer Aljohani (18497914)

“…<div><p>Chest X-ray image classification plays an important role in medical diagnostics. Machine learning algorithms enhanced the performance of these classification algorithms by introducing advance techniques. …”

Internal symmetry in crystallin proteins. by Spencer E. Bliven (6672755)

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Python-based Monte Carlo Simulation Tool by Yangfan Jiang (9372782)

BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data by Jean-Christophe Lachance (6619307)

“…Despite its importance, no standardized computational platform is currently available to generate species-specific biomass objective functions in a data-driven, unbiased fashion. …”

Python-Based Algorithm for Estimating NRTL Model Parameters with UNIFAC Model Simulation Results by Se-Hee Jo (20554623)

“…This algorithm conducts a series of procedures: (1) fragmentation of the molecules into functional groups from SMILES, (2) calculation of activity coefficients under predetermined temperature and mole fraction conditions by employing universal quasi-chemical functional group activity coefficient (UNIFAC) model, and (3) regression of NRTL model parameters by employing UNIFAC model simulation results in the differential evolution algorithm (DEA) and Nelder–Mead method (NMM). …”

Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein–Ligand Binding Poses by Dominykas Lukauskis (14143149)

“…Predicting the correct pose of a ligand binding to a protein and its associated binding affinity is of great importance in computer-aided drug discovery. …”

Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein–Ligand Binding Poses by Dominykas Lukauskis (14143149)

“…Predicting the correct pose of a ligand binding to a protein and its associated binding affinity is of great importance in computer-aided drug discovery. …”

Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein–Ligand Binding Poses by Dominykas Lukauskis (14143149)

“…Predicting the correct pose of a ligand binding to a protein and its associated binding affinity is of great importance in computer-aided drug discovery. …”

Components of a CCA function. by Hiam Alquran (17636906)

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Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm by Spencer E. Bliven (6672755)

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<b>Opti2Phase</b>: Python scripts for two-stage focal reducer by Morgan Najera (21540776)

“…</li></ul><p dir="ltr">The scripts rely on the following Python packages. Where available, repository links are provided:</p><ol><li><b>NumPy</b>, version 1.22.1</li><li><b>SciPy</b>, version 1.7.3</li><li><b>PyGAD</b>, version 3.0.1 — https://pygad.readthedocs.io/en/latest/#</li><li><b>bees-algorithm</b>, version 1.0.2 — https://pypi.org/project/bees-algorithm</li><li><b>KrakenOS</b>, version 1.0.0.19 — https://github.com/Garchupiter/Kraken-Optical-Simulator</li><li><b>matplotlib</b>, version 3.5.2</li></ol><p dir="ltr">All scripts are modular and organized to reflect the design stages described in the manuscript.…”