Related Experiment Video
Updated: Apr 14, 2026
05:08
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
1.4K
DOCKSCORE: a webserver for ranking protein-protein docked poses
Sony Malhotra1, Oommen K Mathew2,3, Ramanathan Sowdhamini4
1National Centre for Biological Sciences (TIFR), UAS-GKVK Campus, Bellary Road, Bangalore, 560 065, India. sonym@ncbs.res.in.
BMC Bioinformatics
|April 24, 2015
Summary
DockScore is a new webserver that ranks protein-protein docked poses using interface parameters. This tool helps researchers identify the most accurate protein interaction models from computational docking results.
Area of Science:
- Computational biology
- Structural bioinformatics
Background:
- Protein-protein interactions are crucial for cellular functions but challenging to study structurally.
- Computational docking predicts interaction modes but requires accurate scoring to identify native poses.
- DockScore is a scoring scheme that evaluates interface properties like surface area, conservation, and clustering.
Purpose of the Study:
- To develop and provide a user-friendly webserver implementation of the DockScore scoring scheme.
- To assist researchers in ranking and selecting accurate protein-protein docked poses.
Main Methods:
- Implementation of the DockScore algorithm as a webserver.
- Input of multiple docked poses for scoring.
- Analysis of interface parameters including surface area, evolutionary conservation, hydrophobicity, short contacts, and spatial clustering.
Main Results:
- The DockScore webserver successfully scores and ranks multiple docked poses.
- Results include scores, ranks, and downloadable CSV files.
- A graphical interface visualizes the best-ranking poses and their interfaces.
Conclusions:
- The DockScore webserver is a valuable tool for the scientific community.
- It facilitates the selection of native or near-native protein-protein interaction poses.
- The webserver is freely accessible for research purposes.
More Related Videos
Related Concept Videos
02:04Protein-protein Interfaces
15.0K
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
02:04Protein-Protein Interfaces
4.6K
4.6K
02:40Ligand Binding Sites
15.9K
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...
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...
15.9K
02:40Ligand Binding Sites
9.1K
9.1K
01:49Conserved Binding Sites
5.3K
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...
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
02:26Protein Networks
4.7K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.7K