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)

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

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)

“…</p><p dir="ltr">The package includes:</p><ul><li>Scripts for first-order analysis, third-order modeling, optimization using a Physically Grounded Merit Function (PGMF), and RMS-based refinement.</li><li>A subfolder named <b>Images</b>, which stores the figures generated by six of the seven provided scripts.…”

How fries chooses which sequences to keep and which sequences to prune. by Anna U. Lowegard (8051597)

Subjects:

Data from: Structural and Functional Analysis of Multi-interface Domains by ZHAO Liang (8657694)

“…This work applies graph theory and algorithms to discover fingerprints for the multiple interfaces of a domain and to establish associations between the interfaces and functions, based on a huge set of multi-interface proteins from PDB. …”

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

Subjects:

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

“…<i>(b)</i> Metabolic byproducts move the relevant unperturbed state from <b>R</b>⁰ (gray ‘x’) to (black ‘x’), which is itself a function of the current environmental conditions. …”

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. …”

Flexible CDOCKER: Hybrid Searching Algorithm and Scoring Function with Side Chain Conformational Entropy by Yujin Wu (2901128)

“…We test our developments by considering five protein targets, thrombin, dihydrofolate reductase­(DHFR), T4 L99A, T4 L99A/M102Q, and PDE10A, which belong to different enzyme classes with different binding pocket environments, as a representative set of diverse ligands and receptors. …”

Flexible CDOCKER: Hybrid Searching Algorithm and Scoring Function with Side Chain Conformational Entropy by Yujin Wu (2901128)

“…We test our developments by considering five protein targets, thrombin, dihydrofolate reductase­(DHFR), T4 L99A, T4 L99A/M102Q, and PDE10A, which belong to different enzyme classes with different binding pocket environments, as a representative set of diverse ligands and receptors. …”

The GOR4 and SOPMA algorithm findings. by Ahmad Abdullah Mahdeen (19704401)

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

Algorithmic assessment reveals functional implications of GABRD gene variants linked to idiopathic generalized epilepsy by Ayla Arslan (17943365)

“…</p> <p>The study identifies specific variants (L111R, R114C, D123N, G150S, and L243P) in the coding region of the GABRD gene, which are predicted as deleterious by multiple algorithms. …”

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)

Depiction of the theory, can sequence infer function? by Ashley I. Heinson (8124374)

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

NRPStransformer, an Accurate Adenylation Domain Specificity Prediction Algorithm for Genome Mining of Nonribosomal Peptides by 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. …”