IISc GraProtS

Network Analysis Based Quality Assessement for modelled structures

    This module (PSN-QA) ofGraProStr evaluates a protein structure (PDB, modelled, decoy) from its network perspective. The network has been constructed on the basis of non-covalent interactions between side chains of the polypeptide chain.

    Please cite the following paper for this module:

    Chatterjee S, Ghosh S, Vishveshwara S, Network properties of decoys and CASP predicted models: a comparison with native protein structures. Mol. BioSyst., 2013,9, 1774-1788

    This module consist of two programs : 1) Native/Non-native Classification and 2) Native/Non-native Rank

    Program 1 evaluates the network parameters and decides whether the protein structure is native or non-native. Various output files, network parameter files and graphs displaying the transition profiles are available for download in this case.

    In program 2, instead of the binary classification as provided in Program1, a quantitative ranking for each models are provided. At a given time, 5 such models can be uploaded. This program ranks the models based on how close the structure is to a native protein structure. Generally, ranks above 16 and below 10 are considered as native or non-native like respectively.

    For structures with ranks between 10 and 16, program 1 can be used to probe the structure in details and finally to evaluate the state of the structure. Both the programs are trained using a large number of PDB crystal structures (with resolution lower than 3A) and many decoy structures from a large number of decoy datasets.

    Please note that the method works best in detecting compact, globular proteins.

    • External resources implemented in the methodology:

      1. LIBSVM [Copyright (c) 2000-2013 Chih-Chung Chang and Chih-Jen Lin. All rights reserved]: Chih-Chung Chang and Chih-Jen Lin, LIBSVM : a library for support vector machines. ACM Transactions on Intelligent Systems and Technology, 2:27:1--27:27, 2011. Software available at http://www.csie.ntu.edu.tw/~cjlin/libsvm

      2. LIBLINEAR: Copyright (c) 2007-2013 The LIBLINEAR Project. All rights reserved.

      2. HBPlus: I.K. McDonald and J.M. Thornton (1994), "Satisfying Hydrogen Bonding Potential in Proteins", JMB 238:777-793.

      3. CFinder: Palla et. al., Nature 435, 814-818 (2005)

      4. Gnuplot [Copyright 1986 - 1993, 1998, 2004 Thomas Williams, Colin Kelley]

Developed and Maintained by SOMA GHOSH (soma@mbu.iisc.ernet.in)