Editorial [Hot Topic: Protein Peptide Informatics and Drug Designing - Some Computational Techniques for Structural Genomics Based Approaches (Part II) (Guest Editor: Rajani R. Joshi)]

This is the second and concluding part of the special issue of “Protein Peptide Letters” which presents some state-of-the art contributions in multi-dimensional research at the interface of Protein Peptide Informatics and Drug Designing. The first part focused at specific experimental and computational studies on Protein Kinases, GRPs, and peptide based vaccine designs and structuralbinding properties of several drug targets in Plasmodium falciparum, HIV-I and Japanese Encephalitis Virus. This issue presents some novel algorithms, computational techniques, servers, softwares and databases providing wider applications in Structure Based Drug Design (SBDD) and related issues in Genomics and Proteomics. Drug development research in the past decades has focused on the enzyme-binding-pocket model of drug targets. Advances headed towards peptide and gene based rational drug and vaccine designs now require knowledge of the structural biology of the target, co-receptor and inhibitor molecules. The ab-initio method (PEPstr) and corresponding web-server developed by H. Kaur, A. Garg and G. P. S. Raghava for prediction of tertiary structure of small bioactive peptides makes a useful contribution in this context. Prediction and analysis of the binding interactions of the drug with the receptor (target) molecules is crucial in drug designing projects. Computational methods based on surface complementarity and stereochemistry are widely used for this purpose to enable docking of protein - protein and protein - ligands. However, modifications in the existing docking algorithms are often required in deciphering the stochastic interactions that account for diversity and affinity in surface-complementarity. The all-atom based Monte Carlo method and useful application software named ParDOCK developed by Prof. B. Jayaram's research group in the supercomputing lab at IIT Delhi is an important contribution in this regard. The paper by A. Gupta, A. Gandhimathi, P. Sharma and B. Jayaram presents this procedure with validation results and applications. The applications and scope of gene and protein data banks in next generation research and development in Medical Biotechnology and Pharmacology are remarkable. Multiple sequence alignment and homology modeling have no doubt made the major chunk of harvesting the fruits of knowledge from the ever-expanding databases of experimental data on the Internet. However these datamining techniques are not limitation-free to meet the challenges of Nature. The innovative approach of alignment-free classification of protein sequences presented in the paper by S. Deshmukh, S. Khaitan, D. Das, M. Gupta and P. P. Wangikar provides a distinct alternative with significant scope. Dr. Wangikar's research group had recently reported a new method of classifying protein structure using geometrically invariant structural patterns. Extended application of this algorithm together with dynamic programming, as reported in his paper with A. Dalal and S. Deshmukh, provides an efficient method for protein structure alignment. This method is found to reduce the computational time by 30 to 60 times as compared to the execution time of the conventional methods for average sized protein chains. Two useful contributions to protein structure modeling, analysis or comparison of specific structural attributes are made by Dr. Sekar's group, viz - (i) comprehensive data base (CADB-3.0) of conformation angles of known protein structures (ii) advanced web server for online display of Ramchandran Plot of the confirmation angles of the polypeptide chain of a protein with demarcation of secondary structural elements and regions within any given set or range of values of these angels. Applications illustrated in the corresponding papers - (i) by K. Gopalakrishnan, S. S. Sheik, C. Vasuki Ranjani, A. Udayakumar and K. Sekar; and (ii) K. Gopalakrishnan, G. Sowmiya, S. S. Sheik and K. Sekar - include targets of certain drugs. C. Ramakrishnan, B. Lakshmi, A. Kurien, D. Devipriya and Dr. N. Srinivasan have analyzed the presence of conformational angles (,φ) in non-redundant, high resolution crystal structures of proteins and peptides focusing on those ranges of pair of these angles that are disallowed in the Ramchandran plots....