Functional effect prediction of FUS mutations by ten nsSNP prediction algorithms. by L. F. S. Bonet (11502082)

Radius of gyration (RG) of the backbone atoms of the protein as a function of time. by L. F. S. Bonet (11502082)

Solvent-accessible surface area (SASA) of the protein as a function of time. by L. F. S. Bonet (11502082)

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

Subjects:

Immune infiltration analysis by CIBERSORT algorithm. by Lanying Shen (22755930)

Immune infiltration analysis by CIBERSORT algorithm. by Lanying Shen (22755930)

Root mean square deviation (RMSD) of the backbone atoms of the protein as a function of time. by L. F. S. Bonet (11502082)

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

Subjects:

Python implementation of the Trajectory Adaptive Multilevel Sampling algorithm for rare events and improvements by Pascal Wang (10130612)

“…<div>This directory contains Python 3 scripts implementing the Trajectory Adaptive Multilevel Sampling algorithm (TAMS), a variant of Adaptive Multilevel Splitting (AMS), for the study of rare events. …”

Root mean square fluctuation (RMSF) of the backbone atoms of the protein as a function of each amino acid residue. by L. F. S. Bonet (11502082)

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)

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

Pairwise alignment results from human proteins and <i>H</i>. <i>pylori</i> proteins using Blosum 62 and PM250 algorithms. by Andrés Sánchez Caraballo (15354081)

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)

Illustration of the perturbation of the protein relationship network and NECARE algorithm. by Jiajun Qiu (4684921)

Core genes were selected through PPI analysis based on three algorithms. by Dong-Hee Han (140305)

“…<b>(B)</b> The priority of the top 10 genes was evaluated through MNC, which identifies clusters of protein nodes that are more functionally connected to each other and selects the central proteins within the cluster. …”

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.…”