A comparison of visual tools for the exploration of biomolecular networks. حسب Paolo Perlasca (9909695)

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Starting point of the community-based navigation. حسب Paolo Perlasca (9909695)

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Fig 7 - حسب Paolo Perlasca (9909695)

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Top 3-enriched pathways with literature evidence. حسب Paolo Perlasca (9909695)

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

Co-simulation architecture. حسب Honglei Pang (22693724)

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

Sub-model-specific gene sets with functional annotations and weights. حسب Josh L. Espinoza (10492448)

Network-aware functional overrepresentation results. حسب Agatha Treveil (10090931)

SARS-CoV-2—human protein complex map showing complexes identified by Super.Complex. حسب Meghana Venkata Palukuri (11890672)

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

Identification and functional analysis of hub genes. حسب Wei Ya Lan (22403712)

"…<p>(A) Protein–protein interaction (PPI) network constructed using the STRING database with a confidence score > 0.04. …"

Python-Based Algorithm for Estimating NRTL Model Parameters with UNIFAC Model Simulation Results حسب 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). …"

Alignment of amino-acids sequence of nucleotide-binding domains of Ssa1 with DnaK from <i>E</i>. <i>coli</i> using the Needleman-Wunsch algorithm for global alignment. حسب Deepika Gaur (814560)

<b>Opti2Phase</b>: Python scripts for two-stage focal reducer حسب 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.…"

Functional enrichment of protein subnetworks in HIV-1 producer cells after co-culture with uninfected cells. حسب James W. Bruce (10204626)

Discovery of Protein Modifications Using Differential Tandem Mass Spectrometry Proteomics حسب 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 حسب 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. …"

Revisiting the “satisfaction of spatial restraints” approach of MODELLER for protein homology modeling حسب Giacomo Janson (8138517)

"…<div><p>The most frequently used approach for protein structure prediction is currently homology modeling. …"

Main parameters of braking system. حسب Honglei Pang (22693724)

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