scholarly journals Geometrical eigen-subspace framework based molecular conformation representation for efficient structure recognition and comparison

2017 ◽  
Vol 146 (15) ◽  
pp. 154108 ◽  
Author(s):  
Xiao-Tian Li ◽  
Xiao-Bao Yang ◽  
Yu-Jun Zhao
Keyword(s):  
Molecular Conformation ◽  
Structure Recognition

Homologation: A Versatile Molecular Modification Strategy to Drug Discovery

2019 ◽  
Vol 19 (19) ◽  
pp. 1734-1750 ◽  
Author(s):  
Lídia M. Lima ◽  
Marina A. Alves ◽  
Daniel N. do Amaral
Keyword(s):  
Protein Structure ◽  
Homologous Series ◽  
Molecular Conformation ◽  
Chemical Properties ◽  
Lead Optimization ◽  
Pharmacokinetic Property ◽  
Molecular Modification ◽  
Physico Chemical ◽  
Pharmacokinetic Properties ◽  
Lead Identification

Homologation is a concept introduced by Gerhard in 1853 to describe a homologous series in organic chemistry. Since then, the concept has been adapted and used in medicinal chemistry as one of the most important strategies for molecular modification. The homologation types, their influence on physico-chemical properties and molecular conformation are presented and discussed. Its application in lead-identification and lead optimization steps, as well as its impact on pharmacodynamics/pharmacokinetic properties and on protein structure is highlighted from selected examples. <p> • Homologation: definition and types <p> • Homologous series in nature <p> • Comparative physico-chemical and conformational properties <p> • Application in lead-identification and lead-optimization <p> • Impact on pharmacodynamic property <p> • Impact on pharmacokinetic property <p> • Impact on protein structure <p> • Concluding remarks <p> • Acknowledgment <p> • References

Temperature Dependence of Molecular Conformation, Dynamics, and Chemical Shift Anisotropy of α,α-Trehalose in D2O by NMR Relaxation

1997 ◽  
Vol 119 (6) ◽  
pp. 1336-1345 ◽  
Author(s):  
Gyula Batta ◽  
Katalin E. Kövér ◽  
Jacquelyn Gervay ◽  
Miklós Hornyák ◽  
Gareth M. Roberts
Keyword(s):  
Chemical Shift ◽  
Temperature Dependence ◽  
Molecular Conformation ◽  
Chemical Shift Anisotropy ◽  
Nmr Relaxation

Vibrational spectra and molecular conformation of ciliatine

1993 ◽  
Vol 298 ◽  
pp. 1-11 ◽  
Author(s):  
Keiichi Ohno ◽  
Yoshitaka Mandai ◽  
Hiroatsu Matsuura
Keyword(s):  
Vibrational Spectra ◽  
Molecular Conformation

scholarly journals Two Decades of 4D-QSAR: A Dying Art or Staging a Comeback?

2021 ◽  
Vol 22 (10) ◽  
pp. 5212
Author(s):  
Andrzej Bak
Keyword(s):  
Molecular Conformation ◽  
Graphics Processing Unit ◽  
Processing Unit ◽  
Diverse Range ◽  
Current State ◽  
Gpu Clusters ◽  
Pharmacophore Hypothesis ◽  
Rising Power ◽  
Graphics Processing ◽  
Ligand Conformation

A key question confronting computational chemists concerns the preferable ligand geometry that fits complementarily into the receptor pocket. Typically, the postulated ‘bioactive’ 3D ligand conformation is constructed as a ‘sophisticated guess’ (unnecessarily geometry-optimized) mirroring the pharmacophore hypothesis—sometimes based on an erroneous prerequisite. Hence, 4D-QSAR scheme and its ‘dialects’ have been practically implemented as higher level of model abstraction that allows the examination of the multiple molecular conformation, orientation and protonation representation, respectively. Nearly a quarter of a century has passed since the eminent work of Hopfinger appeared on the stage; therefore the natural question occurs whether 4D-QSAR approach is still appealing to the scientific community? With no intention to be comprehensive, a review of the current state of art in the field of receptor-independent (RI) and receptor-dependent (RD) 4D-QSAR methodology is provided with a brief examination of the ‘mainstream’ algorithms. In fact, a myriad of 4D-QSAR methods have been implemented and applied practically for a diverse range of molecules. It seems that, 4D-QSAR approach has been experiencing a promising renaissance of interests that might be fuelled by the rising power of the graphics processing unit (GPU) clusters applied to full-atom MD-based simulations of the protein-ligand complexes.

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