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)

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

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The “Bubblepole” (BUPO) Method for Linear-Scaling Coulomb Matrix Construction with or without Density Fitting by Frank Neese (736441)

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

Genetic algorithms can be applied to higher-dimensional design problems. by Lu Hong (399882)

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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)

Gene pairs with or without known protein-protein interactions in Reactome. by Halima Alachram (11570633)

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Histograms of genes with or without known Reactome protein-protein interactions. by Halima Alachram (11570633)

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Cost functions implemented in Neuroptimus. by Máté Mohácsi (20469514)

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

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). …”

<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.…”

Discovery of Protein Modifications Using Differential Tandem Mass Spectrometry Proteomics by Paolo Cifani (1575613)

“…Termed SAMPEI for spectral alignment-based modified peptide identification, this open-source algorithm is designed for the discovery of functional protein and peptide signaling modifications, without prior knowledge of their identities. …”

Discovery of Protein Modifications Using Differential Tandem Mass Spectrometry Proteomics by Paolo Cifani (1575613)

“…Termed SAMPEI for spectral alignment-based modified peptide identification, this open-source algorithm is designed for the discovery of functional protein and peptide signaling modifications, without prior knowledge of their identities. …”

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

“…OpenBPMD is powered by the OpenMM simulation engine and uses a revised scoring function. The algorithm was validated by testing it on a wide range of targets and showing that it matches or exceeds the performance of the original BPMD. …”

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

“…OpenBPMD is powered by the OpenMM simulation engine and uses a revised scoring function. The algorithm was validated by testing it on a wide range of targets and showing that it matches or exceeds the performance of the original BPMD. …”

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

“…OpenBPMD is powered by the OpenMM simulation engine and uses a revised scoring function. The algorithm was validated by testing it on a wide range of targets and showing that it matches or exceeds the performance of the original BPMD. …”

Flowchart of proposed fitness function algorithm. by Ferhat Yuna (21519851)

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Comparison of algorithms in two cases. by Yi Tao (178829)

Subjects: “…evolutionary genetic algorithm…”