Human immunodeficiency virus infection / acquired immunodeficiency syndrome (HIV/AIDS) is a disease pertained to the human immune system. Given its crucial role in viral replication, HIV-1 protease (HIV-1 PR) is a prime therapeutic target in AIDS therapy. In this regard, the dynamic aspects of ligand-enzyme interactions may indicate an important role of conformational variability in HIV-1 PR in...

In this paper we report new results concerning use of genetic algorithms in conformational analysis, field of pharmacy related to discovery and design of new drugs. The goal is to find the optimal spatial configuration of a molecule, which corresponds to finding its energy minimum by rotation of torsion angles. A number of experimental results obtained with different evolutionary mechanisms and...

Aim: This study was designed to develop peptide analogs of Infectious Bursal Disease (IBD) virus VP5 protein segment having cell penetrating ability to improve their interaction with cargo molecule (Nucleic acid) without affecting the backbone conformation. Materials and Methods: IBDV VP5 protein segment designated as RATH peptide were synthesized using solid phase peptide synthesis and their s...

Side chain-to-side chain cyclizations represent a strategy to select a family of bioactive conformations by reducing the entropy and enhancing the stabilization of functional ligand-induced receptor conformations. This structural manipulation contributes to increased target specificity, enhanced biological potency, improved pharmacokinetic properties, increased functional potency, and lowered m...

Correlated motions in biomolecules are often essential for their function, for example, allosteric signal transduction or mechanical/thermodynamic energy transport. Principal component analysis (PCA) is a widely used method to extract functionally relevant collective motions from a molecular dynamics (MD) trajectory. Being based on the covariance matrix, however, PCA detects only linear correla...