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

الموضوعات:

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... حسب Giacomo Janson (8138517)

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

gmxapi usage examples. حسب M. Eric Irrgang (4487278)

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

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

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

Schematics for gmxapi operations. حسب M. Eric Irrgang (4487278)

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

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). …"

<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.…"

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. …"

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

الموضوعات: "…evolutionary genetic algorithm…"

Flow of the NSGA-II algorithm. حسب Yi Tao (178829)

الموضوعات: "…evolutionary genetic algorithm…"

An expectation-maximization algorithm for finding noninvadable stationary states. حسب Robert Marsland (8616483)

Python implementation of the Trajectory Adaptive Multilevel Sampling algorithm for rare events and improvements حسب 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. …"

Pipeline of the interactor algorithm. حسب Jose Cleydson F. Silva (8685594)

Modeling with uniform <i>σ</i> values. حسب Giacomo Janson (8138517)