Explicit treatment of non‐Michaelis‐Menten and atypical kinetics in early drug discovery
B Srinivasan - ChemMedChem, 2021 - Wiley Online Library
Biological systems are highly regulated. They are also highly resistant to sudden
perturbations enabling them to maintain the dynamic equilibrium essential to sustain life …
perturbations enabling them to maintain the dynamic equilibrium essential to sustain life …
Microbial 5′-nucleotidases: their characteristics, roles in cellular metabolism, and possible practical applications
NP Zakataeva - Applied Microbiology and Biotechnology, 2021 - Springer
Nucleotidases (EC 3.1. 3.5) are enzymes that catalyze the hydrolytic dephosphorylation of
5′-ribonucleotides and 5′-deoxyribonucleotides to their respective nucleosides and …
5′-ribonucleotides and 5′-deoxyribonucleotides to their respective nucleosides and …
PASSer2. 0: accurate prediction of protein allosteric sites through automated machine learning
Allostery is a fundamental process in regulating protein activities. The discovery, design, and
development of allosteric drugs demand better identification of allosteric sites. Several …
development of allosteric drugs demand better identification of allosteric sites. Several …
Silver ions caused faster diffusive dynamics of histone-like nucleoid-structuring proteins in live bacteria
AA Sadoon, P Khadka, J Freeland… - Applied and …, 2020 - Am Soc Microbiol
The antimicrobial activity and mechanism of silver ions (Ag+) have gained broad attention in
recent years. However, dynamic studies are rare in this field. Here, we report our …
recent years. However, dynamic studies are rare in this field. Here, we report our …
Chemical space of Escherichia coli dihydrofolate reductase inhibitors: New approaches for discovering novel drugs for old bugs
B Srinivasan*, S Tonddast‐Navaei… - Medicinal research …, 2019 - Wiley Online Library
Escherichia coli Dihydrofolate reductase is an important enzyme that is essential for the
survival of the Gram‐negative microorganism. Inhibitors designed against this enzyme have …
survival of the Gram‐negative microorganism. Inhibitors designed against this enzyme have …
A guide to enzyme kinetics in early drug discovery
B Srinivasan - The FEBS Journal, 2023 - Wiley Online Library
Drugs interact with their target of interest to bring about the desired phenotypic outcome that
results in disease alleviation. Traditionally, most lead optimization exercises were driven by …
results in disease alleviation. Traditionally, most lead optimization exercises were driven by …
Applications of machine learning in computer-aided drug discovery
SMBA Turzo, ER Hantz, S Lindert - QRB discovery, 2022 - cambridge.org
Machine learning (ML) has revolutionised the field of structure-based drug design (SBDD) in
recent years. During the training stage, ML techniques typically analyse large amounts of …
recent years. During the training stage, ML techniques typically analyse large amounts of …
Realization of the structural fluctuation of biomolecules in solution: Generalized Langevin Mode Analysis
M Sugita, F Hirata - Journal of Computational Chemistry, 2023 - Wiley Online Library
A new theoretical method, referred to as Generalized Langevin Mode Analysis (GLMA), is
proposed to analyze the mode of structural fluctuations of a biomolecule in solution. The …
proposed to analyze the mode of structural fluctuations of a biomolecule in solution. The …
Functional annotation of haloacid dehalogenase superfamily structural genomics proteins
LS Pathira Kankanamge, LA Ruffner… - Biochemical …, 2023 - portlandpress.com
Haloacid dehalogenases (HAD) are members of a large superfamily that includes many
Structural Genomics proteins with poorly characterized functionality. This superfamily …
Structural Genomics proteins with poorly characterized functionality. This superfamily …
Self-Effected Allosteric Coupling and Cooperativity in Hypoxic Response Regulation with Disordered Proteins
Hypersensitive regulation of cellular hypoxic response relies on cooperative displacement of
one disordered protein (HIF-1α) by another disordered protein (CITED2) from the target in a …
one disordered protein (HIF-1α) by another disordered protein (CITED2) from the target in a …