Protien modeling 2026

This set of flashcards covers key terms and concepts related to homology modeling in protein structure prediction, drug design, and the computational methods used in these fields.

Homology Modeling

A computational technique used to predict the 3D structure of a protein sequence by leveraging the known structure of a related homologous protein.

Template

A homologous protein with a known 3D structure used as a reference for modeling the target protein.

CADD

Computer-Aided Drug Design; methods used throughout the drug discovery pipeline to optimize and accelerate the drug development process.

vHTS

Virtual High Throughput Screening; computational screening of chemical libraries against a target protein to identify lead compounds.

Docking

Predicts the orientation of a ligand when bound to a protein target, estimating binding affinity.

Pharmacophore

Models that define essential features of a ligand required for optimal interaction with a biological target.

QSAR

Quantitative Structure-Activity Relationship models that establish the relationship between chemical structure and biological activity.

Primary Structure

The linear sequence of amino acids in a protein, dictating higher-order structures.

Secondary Structure

Regular arrangements of the polypeptide backbone, often stabilized by hydrogen bonds, such as alpha-helices and beta-sheets.

Tertiary Structure

The overall 3D fold of a polypeptide chain, including secondary structures and side chains.

Quaternary Structure

The arrangement of multiple polypeptide chains in a protein complex.

Ramachandran Diagram

A graphical representation mapping allowed combinations of backbone dihedral angles for amino acids.

X-ray Crystallography

A technique that determines atomic coordinates of proteins using X-ray diffraction patterns.

NMR Spectroscopy

A method to determine the structures of smaller proteins in solution, providing insights into protein dynamics.

Electron Cryomicroscopy

Allows visualization of larger protein complexes at near-atomic resolution without requiring crystallization.

Loop Modeling

Process of addressing gaps in a protein model due to insertions or deletions by predicting loop regions.

Model Optimization

The energy minimization of a protein model to relieve steric clashes and refine its conformation.

Model Validation

Assessment of the 3D protein model's accuracy and quality using various metrics.

SWISS-MODEL

An automated web server known for user-friendliness in homology modeling.

Fold Recognition (Threading)

A method used when sequence similarity is low to determine potential structural scaffolds.

Ab Initio Prediction

Predicting protein structures from scratch based solely on amino acid sequence without templates.

AlphaFold

A deep learning-based method by DeepMind for accurate protein structure prediction.