QM/MM methods for biomolecular systems

HM Senn, W Thiel - Angewandte Chemie International Edition, 2009 - Wiley Online Library
Two are better than one: Quantum mechanics/molecular mechanics (QM/MM) methods are
the state‐of‐the‐art computational technique for treating reactive and other “electronic” …

Ligand-binding affinity estimates supported by quantum-mechanical methods

U Ryde, P Soderhjelm - Chemical Reviews, 2016 - ACS Publications
One of the largest challenges of computational chemistry is calculation of accurate free
energies for the binding of a small molecule to a biological macromolecule, which has …

Molecular dynamics investigation on a series of HIV protease inhibitors: assessing the performance of MM-PBSA and MM-GBSA approaches

HK Srivastava, GN Sastry - Journal of chemical information and …, 2012 - ACS Publications
The binding free energies (Δ G Bind) obtained from molecular mechanics with Poisson–
Boltzmann surface area (MM-PBSA) or molecular mechanics with Generalized Born surface …

QM/MM approaches in medicinal chemistry research

LC Menikarachchi, JA Gascón - Current Topics in Medicinal …, 2010 - ingentaconnect.com
One of the goals of medicinal chemistry concerns the ability to compute protein-ligand
interactions based on the structural knowledge of the receptor. To this end, the majority of …

QM/MM‐Methoden für biomolekulare Systeme

HM Senn, W Thiel - Angewandte Chemie, 2009 - Wiley Online Library
Quantenmechanische/molekülmechanische (QM/MM‐) Verfahren sind die Methode der
Wahl für die theoretische Behandlung reaktiver oder anderer elektronischer Prozesse in …

Exquisite Selectivity for Human Toll-Like Receptor 8 in Substituted Furo[2,3-c]quinolines

HP Kokatla, D Sil, SS Malladi… - Journal of medicinal …, 2013 - ACS Publications
Toll-like receptor (TLR)-8 agonists activate adaptive immune responses by inducing robust
production of T helper 1-polarizing cytokines, suggesting that TLR8-active compounds may …

Design, Synthesis, and Biological Evaluation of Novel Hybrid Dicaffeoyltartaric/Diketo Acid and Tetrazole-Substituted l-Chicoric Acid Analogue Inhibitors of Human …

DC Crosby, X Lei, CG Gibbs… - Journal of medicinal …, 2010 - ACS Publications
Fourteen analogues of the anti-HIV-1 integrase (IN) inhibitor l-chicoric acid (L-CA) were
prepared. Their IC50 values for 3′-end processing and strand transfer against recombinant …

Human Toll-Like Receptor 8-Selective Agonistic Activities in 1-Alkyl-1H-benzimidazol-2-amines

M Beesu, SS Malladi, LM Fox, CD Jones… - Journal of medicinal …, 2014 - ACS Publications
Toll-like receptor (TLR)-8 agonists strongly induce the production of T helper 1-polarizing
cytokines and may therefore serve as promising candidate vaccine adjuvants, especially for …

SQM/COSMO Scoring Function: Reliable Quantum‐Mechanical Tool for Sampling and Ranking in Structure‐Based Drug Design

A Pecina, SM Eyrilmez, C Köprülüoğlu… - …, 2020 - Wiley Online Library
Quantum mechanical (QM) methods have been gaining importance in structure‐based drug
design where a reliable description of protein‐ligand interactions is of utmost significance …

The catalytic mechanism of glyceraldehyde 3-phosphate dehydrogenase from Trypanosoma cruzi elucidated via the QM/MM approach

M Reis, CN Alves, J Lameira, I Tuñón, S Martí… - Physical Chemistry …, 2013 - pubs.rsc.org
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) has been identified as a key
enzyme involved in glycolysis processes for energy production in the Trypanosoma cruzi …