Editorial [Hot topic: Protein Folding, Stability and Interactions (Guest Editor: M. Michael Gromiha)]

Proteins and their interactions play vital roles in living organisms. Elucidating the mechanism of protein folding as well as the recognition of protein complexes are intriguing and challenging problems in protein science. Recent years have shown tremendous advances to our knowledge of protein folding, stability and their interactions. The problem of protein folding, stability and interactions has been viewed through several perspectives using experimental and computational approaches. The special issue on “Protein folding, stability and interactions” is aimed at providing a recent update on the folding and stability of proteins and their interactions with other molecules (proteins, nucleic acids, carbohydrates and ligands). It also addresses the significance of the analysis of protein structures, secondary and tertiary structure predictions and folding rates of proteins. The special issue is broadly classified into two parts; the first part is focused on the aspects of protein folding and stability with seven articles and the second part is devoted to protein interactions, which has five papers. The opening article by Shenoy and Jayaram [1] provided the state of the art in protein three-dimensional structure prediction along with disordered proteins and protein-protein interactions. Gaspari et al. [2] analyzed the dynamically restrained conformational ensemble of proteins generated from residual dipolar coupling data in terms of protruding and buried atoms as well as inter-atomic distances with ubiquitin as an example. Galzitskaya [3] proposed Monte Carlo and Capillarity models for understanding and predicting protein folding rates using protein three-dimensional structures. The overview of SBASE domain library, a curated collection of domain sequences and standard similarity search algorithms, which is based on a simple statistics of the domain similarity network, has been illustrated by Dhir et al. [4]. They showed that this method is especially useful in detecting rare, atypical examples of known domain types which are sometimes missed even by more sophisticated methodologies. Tusnady and Simon [5] discussed the current status of topology prediction in transmembrane helical proteins and the annotation of such proteins in genomic sequences. Verma et al. [6] employed a minimal Distance Constraint Model to predict the stability of a series of lysozyme mutants and proposed probable mutants for characterization. The effects of missense mutations on functional stability have been studied with protein sequence analysis algorithms such as spatial distributions of sequence, evolutionary, and physicochemical conservation by Horst et al. [7]. Rashid et al. [8] developed a support vector machine (SVM) based approach using position specific scoring matrices (PSSM) for identifying the interacting proteins in genomic sequences. The combination of hidden Markov models and support vector machines has been used to predict the interaction sites in genome-wide interaction networks by Bartoli et al. [9]. Zhang et al. [10] analyzed a set of RNA binding proteins and developed a method for identifying the RNA binding residues in proteins using evolutionary conservation and predicted secondary structure and solvent accessibility. The recognition mechanism of protein-RNA complexes has been studied with a novel energy based apporach by Gromiha et al. [11]. Carugo and Carugo [12] reviewed the structures of human filamin with emphasis on the relationship between structure, function and interaction. In essence, this special issue comprehends the exciting developments in the area of protein folding, stability and interactions, and it will be a valuable resource for computational biologists, biochemists, biophysicists, bioinformaticians and researchers working in the field of proteins. I would like to thank all the authors for their outstanding contributions and cooperation to complete the task. The guest editor also thanks the Editor-in-Chief Professor Ben M. Dunn for his invitation, encouragement, and support for the successful completion of the special issue.