PROFOUND uses positive-unlabeled classifiers utilizing fold level attributes, environment-specific properties, and deletion site-specific properties to predict the change in foldability owing to contiguous multi-point deletion (MPD) of amino acids in protein structures. PROFOUND is a first of its kind prediction system that reports a recall of 82.2% (86.6%) and a fall out rate of 14.2% (20.6%) corresponding to MPDs in the loop (non-loop) region.
Journal of Chemical Information and Modeling 60(12):6679-6690 [PubMed]
Developed for protein structures, ProTSPoM uses a combination of Random Forest Regressors and Gradient Boosted Regressors along with residue properties, fold level attributes, environmental compatibility, and evolutionary information to predict the change in Gibbs free energy originating out of single point missense mutations. ProTSPoM outperforms all existing state-of-the-art methods in both the Pearson correlation coefficient and root-mean-squared-error parameters for the S2648, S350, S1925, and p53 databases.
Journal of Chemical Information and Modeling 60(6):3315-3323 [PubMed]
Protein phosphorylation is one of the essential post-translation modifications playing a vital role in the regulation of many fundamental cellular processes. We propose a LightGBM-based computational approach that uses evolutionary, geometric, sequence environment, and amino acid-specific features to decipher phosphate binding sites from a protein sequence.
PROTEINS: Structure, Function, and Bioinformatics 88(2):284-291 [PubMed]
Using biological insights, we construct an evolutionary profile to encode the amino acid variability in different positions of the target protein from its structural homologs. We propose an evolutionary profile guided replica-exchange Monte Carlo search algorithm that ensures faster convergence in protein design using a greedy strategy and confirms appreciable exploration and exploitation of the sequence-structure fitness surface. The simulation terminates dynamically after detective a stagnant situation. A series of sequence and structure level validations establish the goodness of our design.
IEEE/ACM Transactions on Computational Biology and Bioinformatics [PubMed ID: 31329126] [PubMed]
Protein backbone alternation due to insertion/deletion or mutation operation often results in a change of fundamental biophysical properties of proteins. The proposed work intends to encode the protein stability changes associated with single-point deletions (SPDs) of amino acids in proteins. The encoding will help in the primary screening of detrimental backbone modifications before opting for expensive in vitro experimentations.
Journal of Proteome Research 18(3):1402-1410 [PubMed]
NIP_NSc is a software to identify the normalized interface packing and normalized surface complementarity at the protein-protein contacts. The software has shows demonstrated performance in discriminating biological interfaces from non-biological ones. The time-efficient performance of the software allows the integration in the large scale screening of protein-protein contacts.
FEBS Letters 584(6):1163-1168 [PubMed]