<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.…"

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

الموضوعات:

Our algorithms process large data sets within a minute. حسب Manu Aggarwal (15990691)

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)

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

"…<i>(c)</i> Pseudocode for self-consistently computing <b>R</b>* and , which is identical to standard expectation-maximization algorithms employed for problems with latent variables in machine learning.…"

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

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)

Reward function related parameters. حسب Honglei Pang (22693724)

الموضوعات:

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

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

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

الموضوعات:

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). …"

NRPStransformer, an Accurate Adenylation Domain Specificity Prediction Algorithm for Genome Mining of Nonribosomal Peptides حسب Zhihan Zhang (1403308)

"…Leveraging the sequences within the flavodoxin-like subdomain, we developed a substrate specificity prediction algorithm using a protein language model, achieving 92% overall prediction accuracy for 43 frequently observed amino acids, significantly improving the prediction reliability. …"

Morpheus: A fragment-based algorithm to predict metamorphic behaviour in proteins across proteomes حسب Vijay Subramanian (20718933)

"…<p dir="ltr">Supplementary material for Morpheus: A fragment-based algorithm to predict metamorphic behaviour in proteins across proteomes.…"

Development and Evaluation of GlycanDock: A Protein–Glycoligand Docking Refinement Algorithm in Rosetta حسب Morgan L. Nance (10981871)

"…In this work, we introduce <i>GlycanDock</i>, a residue-centric protein–glycoligand docking refinement algorithm developed within the Rosetta macromolecular modeling and design software suite. …"

Development and Evaluation of GlycanDock: A Protein–Glycoligand Docking Refinement Algorithm in Rosetta حسب Morgan L. Nance (10981871)

"…In this work, we introduce <i>GlycanDock</i>, a residue-centric protein–glycoligand docking refinement algorithm developed within the Rosetta macromolecular modeling and design software suite. …"

Development and Evaluation of GlycanDock: A Protein–Glycoligand Docking Refinement Algorithm in Rosetta حسب Morgan L. Nance (10981871)

"…In this work, we introduce <i>GlycanDock</i>, a residue-centric protein–glycoligand docking refinement algorithm developed within the Rosetta macromolecular modeling and design software suite. …"

Development and Evaluation of GlycanDock: A Protein–Glycoligand Docking Refinement Algorithm in Rosetta حسب Morgan L. Nance (10981871)

"…In this work, we introduce <i>GlycanDock</i>, a residue-centric protein–glycoligand docking refinement algorithm developed within the Rosetta macromolecular modeling and design software suite. …"