Center for Computational Natural Sciences and Bioinformatics

Center for Computational Natural Sciences and Bioinformatics (CCNSB) is a research center in IIIT Hyderabad that is involved in teaching and research in the areas of computational chemistry, computational and systems biology, bioinformatics, bio-molecular simulations, nanosciences, statistical mechanics and complex systems. Ever increasing computational power and recent advances in computer science, in fields of distributed computing, networking and database management, have inspired the center to explore the application of these newer technologies and methods to understand the functioning of complex physical, chemical and biological systems.

NAPS: Network Analysis of Protein Structures

Research Area
Protein Structure Analysis
Protein Contact Network, Network Biology
Technology Description
Protein structures can be analyzed by modelling proteins as a network of noncovalent interactions between amino acid residues. This technology provides network based analysis of protein structures (NAPS), that facilitates quantitative and qualitative (visual) analysis of residue-residue interactions in: single chains, protein complex, modelled protein structures and trajectories. The user can specify atom type for network construction, distance range and minimal amino acid separation along the sequence. NAPS provides users with a selection of node(s) and its neighbourhood based on centrality measures, physicochemical properties of amino acids or a cluster of well-connected residues (k-cliques) for further analysis. Visual analysis of interacting domains and protein chains, and shortest path lengths between pairs of residues are additional features that aid in functional analysis. NAPS support various analyses and visualization views for identifying functional residues, provide insight into mechanisms of protein folding, domain-domain and protein-protein interactions for understanding communication within and between proteins. The network representation of proteins provides a systems approach to topological analysis of complex three-dimensional structures irrespective of secondary structure and fold type and provide insights into structure-function relationship.
Type of Work
Software system
Current State of work
Technology designed and implemented, Technology thoroughly tested, Product being developed
Potential Applications
1. Protein structure can be represented as network and analyzed using various network analysis measures to study different problems in protein science such as proteins folding, domain/repeat identification, protein dynamics, identification of key residues, allosteric communication, etc.
Related Publications
1. NAPS: Network Analysis of Protein Structures, Nucleic Acids Res. 2016, 44(W1), W375-82