Protocol
Computational Methods and Tools for Repurposing of Drugs Against Coronaviruses
The conventional drug discovery pipeline involving discovery of a new molecule requires huge investment and long time. Therefore, re-using the existing drugs for new indication which is termed as “drug repurpo...
Chapter
Protein Structure, Dynamics and Assembly: Implications for Drug Discovery
Most of the therapeutic drugs available in the market today, are targeted against proteins. Drug molecules are designed to complement shape, size and electrostatic fingerprints of the functional site of a targ...
Article
Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility
Direct massively parallel sequencing of SARS-CoV-2 genome was undertaken from nasopharyngeal and oropharyngeal swab samples of infected individuals in Eastern India. Seven of the isolates belonged to the A2a c...
Article
Open AccessiPBAvizu: a PyMOL plugin for an efficient 3D protein structure superimposition approach
Protein 3D structure is the support of its function. Comparison of 3D protein structures provides insight on their evolution and their functional specificities and can be done efficiently via protein structure...
Article
Open AccessInterface residues of transient protein-protein complexes have extensive intra-protein interactions apart from inter-protein interactions
Protein-protein interactions are crucial for normal biological processes and to regulate cellular reactions that affect gene expression and function. Several previous studies have emphasized the roles of resid...
Protocol
Repurposing Drugs Based on Evolutionary Relationships Between Targets of Approved Drugs and Proteins of Interest
Drug repurposing has garnered much interest as an effective method for drug development among biopharmaceutical companies. The availability of information on complete sequences of genomes and their associated ...
Article
Open AccessUse of designed sequences in protein structure recognition
Knowledge of the protein structure is a pre-requisite for improved understanding of molecular function. The gap in the sequence-structure space has increased in the post-genomic era. Grouping related protein s...
Article
Open AccessExploring anti-malarial potential of FDA approved drugs: an in silico approach
The critically important issue on emergence of drug-resistant malarial parasites is compounded by cross resistance, where resistance to one drug confers resistance to other chemically similar drugs or those th...
Article
Open AccessRecognition of a structural domain (RWDBD) in Gcn1 proteins that interacts with the RWD domain containing proteins
The protein Gcn1 (General control non-derepressible 1) is found in virtually all eukaryotes, and is a key component of the general amino acid control signal transduction pathway. This pathway is best known for...
Article
Open AccessComputational recognition and analysis of hitherto uncharacterized nucleotide cyclase-like proteins in bacteria
Evolutionary relationship between class III nucleotide cyclases and an uncharacterized set of bacterial proteins from Actinobacteria, Bacteroidetes and Proteobacteria has been recognized and analyzed. Detailed...
Protocol
Classification of Protein Kinases Influenced by Conservation of Substrate Binding Residues
With the advent of genome sequencing projects in the recent past, several kinases have come to light as regulating different signaling pathways. These kinases are generally classified into different subfamilie...
Protocol
Improving the Accuracy of Fitted Atomic Models in Cryo-EM Density Maps of Protein Assemblies Using Evolutionary Information from Aligned Homologous Proteins
Cryo-Electron Microscopy (cryo-EM) has become an important technique to obtain structural insights into large macromolecular assemblies. However the resolution of the density maps do not allow for its interpre...
Article
Open AccessDe-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods
In the post-genomic era where sequences are being determined at a rapid rate, we are highly reliant on computational methods for their tentative biochemical characterization. The Pfam database currently contai...
Article
Open AccessCLAP: A web-server for automatic classification of proteins with special reference to multi-domain proteins
The function of a protein can be deciphered with higher accuracy from its structure than from its amino acid sequence. Due to the huge gap in the available protein sequence and structural space, tools that can...
Protocol
Recognition of Nontrivial Remote Homology Relationships Involving Proteins ofHelicobacter pylori: Implications for Function Recognition
This chapter explains techniques for recognition of nontrivial remote homology relationships involving proteins ofHelicobacter pyloriand their implications for function recognition. Using the remote homology de...
Article
Open AccessThe origins of the evolutionary signal used to predict protein-protein interactions
The correlation of genetic distances between pairs of protein sequence alignments has been used to infer protein-protein interactions. It has been suggested that these correlations are based on the signal of c...
Article
Open AccessStructural and molecular basis of interaction of HCV non-structural protein 5A with human casein kinase 1α and PKR
交互的非结构蛋白5 a (NS5A)Hepatitis C virus (HCV) with human kinases namely, casein kinase 1α (ck1α) and protein kinase R (PKR) have different functional implications such as regulatio...
Article
Cis–transpeptide variations in structurally similar proteins
The presence of energetically less favourablecispeptides in protein structures has been observed to be strongly associated with its structural integrity and function. Inter-conversion between thecisandtrans...
Article
Open AccessComparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins
Most signalling and regulatory proteins participate in transient protein-protein interactions during biological processes. They usually serve as key regulators of various cellular processes and are often stabl...
Article
Open AccessAlignHUSH: Alignment of HMMs using structure and hydrophobicity information
Sensitive remote homology detection and accurate alignments especially in the midnight zone of sequence similarity are needed for better function annotation and structural modeling of proteins. An algorithm, A...