Bioshift

Standard molecular docking with AutoDock Vina CPU version

CUDA-accelerated Vina for high-throughput virtual screening

Automated protein preparation for docking (PDBQT conversion)

Ligand preparation with charge and torsion assignment

Parse and analyze docking results with scoring metrics

Split multi-model PDBQT files from docking results

Define search box parameters for docking simulations

Combine multiple molecular structures into single file

Generate topology and prepare system with pdb2gmx

Energy minimization using steepest descent algorithm

NVT and NPT ensemble equilibration protocols

Production MD runs with mdrun engine

RMSD, RMSF, radius of gyration trajectory analysis

Import CHARMM-GUI generated system files

Edit molecular dynamics parameter (.mdp) files

Extract frames from compressed trajectory files

Plot energy, temperature, pressure from .edr files

NGL.js-based trajectory visualization

UFF or MMFF94 force field minimization

Multiple force field options (GAFF, MMFF94, UFF)

Generate low-energy 3D conformers with ETKDG

Split data with stratification support

Scikit-learn logistic regression with regularization

Ensemble tree classifier with feature importance

Support Vector Classification with RBF/linear kernels

K-nearest neighbors with distance metrics

Ordinary least squares linear regression

Ensemble tree regressor for continuous targets

Support Vector Regression with kernel tricks

Pickle-based model serialization

Batch prediction and model evaluation

Column selection, row filtering, sorting operations

Join dataframes and remove duplicate rows

Partition data into K clusters with elbow method

Hierarchical clustering with dendrogram

Principal Component Analysis for feature reduction

Confusion matrix, precision/recall, MSE/R²

Fetch ADMET properties via ADMETLAB 3.0 API

Parse and visualize ADMET prediction results

ProTox-III toxicity class and LD50 prediction

Toxicity endpoint analysis and alerts

Drug-likeness and molecular properties

Property radar charts and rule-of-five

RDKit-based 2D structure depiction

Protein-ligand interaction fingerprinting

NGL.js molecular viewer in embedded browser

SDF, MOL, MOL2, PDB, PDBQT, XYZ with RDKit

CSV, Excel, TXT, JSON with pandas

Save molecules, dataframes, plots, text

Search compounds by name/SMILES/InChI

Fetch protein structures by PDB ID

Extract natural product data

Select subset of DataFrame columns

Filter rows by column conditions

Extract rows by index range

Remove duplicate rows by column values

Sort DataFrame by one or more columns

SQL-style joins (inner, outer, left, right)

Read chromatography data files

Savitzky-Golay and moving average filters

Polynomial and asymmetric least squares

Scipy peak detection with parameters

Peak area and height calculation

Plotly-based chromatogram viewer

Prepare factorial design matrix

Fit polynomial response surface models

Interactive 3D surface and contour plots

Load pickled scikit-learn models

Serialize models to disk

Evaluate model on test data

Generate predictions on new data