Related Experiment Video

Updated: Mar 27, 2026

Pharmacophore Modeling for Targets with Extensive Ligand Libraries: A Case Study on SARS-CoV-2 Mpro
05:50

Pharmacophore Modeling for Targets with Extensive Ligand Libraries: A Case Study on SARS-CoV-2 Mpro

Published on: September 26, 2025

2.0K

Comparative Modeling, Molecular Docking, and Revealing of Potential Binding Pockets of RASSF2; a Candidate Cancer

Sonia Kanwal1, Farrukh Jamil1, Ahmad Ali1

  • 1Department of Biosciences, COMSATS Institute of Information Technology, Sahiwal, Pakistan.

Interdisciplinary Sciences, Computational Life Sciences
|January 20, 2016
PubMed

Insights

RAS-association domain family protein 2 (RASSF2) acts as a tumor suppressor by regulating apoptosis and cell cycle arrest. This study modeled RASSF2 structures to identify potential cancer drug targets.

Area of Science:

  • Molecular Biology
  • Structural Biology
  • Computational Chemistry

Background:

  • The RAS-association domain family protein 2 (RASSF2) is a potential tumor suppressor gene involved in apoptosis and cell cycle arrest.
  • RASSF2 functions as a KRAS-specific effector protein and stabilizes STK3/MST2, playing a crucial role in cancer inhibition.

Purpose of the Study:

  • To generate and validate 3D structural models of RASSF2 using homology modeling.
  • To identify potential drug ligands for RASSF2 through molecular docking studies to understand its function and aid drug discovery.

Main Methods:

  • Homology modeling using MODELLER (9v15) and web servers (I-Tasser, SwissModel, 3D-JigSaw, ModWeb).
  • Model evaluation using various tools.
  • Identification of binding pockets using Site Hound.
  • Molecular docking simulations using AutoDock Vina and AutoDock4.

Main Results:

  • Multiple 3D structural models of RASSF2 were generated and compared.
  • The study identified specific compounds exhibiting high-affinity binding and low binding energy to RASSF2's predicted binding domain.
  • These findings suggest potential regulatory roles for the identified compounds.

Conclusions:

  • The generated RASSF2 structural model is reliable for further structural and functional studies.
  • The identified binding pockets and ligands provide valuable insights for drug discovery targeting RASSF2 in cancer treatment.
  • In silico analysis of binding sites is pivotal for determining protein function and advancing cancer research.
Keywords:
Binding domainsCancerHomology modelingMolecular docking analysesRASSF2

More Related Videos

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

1.3K
A Protocol for Computer-Based Protein Structure and Function Prediction16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

70.1K

Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
5.3K
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
15.7K
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
5.9K
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
15.0K