Lessons in Molecular Recognition. 2. Assessing and Improving Cross-Docking Accuracy

2007 ◽  
Vol 47 (6) ◽  
pp. 2293-2302 ◽  
Author(s):  
Jeffrey J. Sutherland ◽  
Ravi K. Nandigam ◽  
Jon A. Erickson ◽  
Michal Vieth
Keyword(s):  
Molecular Recognition ◽  
Cross Docking ◽  
Docking Accuracy

SELECTION OF BEST CRYSTAL STRUCTURE FOR INITIATING DOCKING-BASED VIRTUAL SCREENING STUDIES OF CDK2 INHIBITORS: A CROSS-DOCKING AND DUD SET VALIDATION APPROACH

INDIAN DRUGS ◽  
2019 ◽  
Vol 56 (06) ◽  
pp. 77-85
Author(s):  
A. Joshi ◽  
◽  
H Bhojwani ◽  
U Joshi
Keyword(s):  
Crystal Structure ◽  
Virtual Screening ◽  
Crystal Structures ◽  
Active Site ◽  
Docking Studies ◽  
Cross Docking ◽  
Screening Protocol ◽  
Initial Crystal ◽  
Docking Accuracy ◽  
Selection Of

A total of 95 crystal structures of CDK2 were selected after considering criteria such as resolution and absence of missing residues in the active site; and subjected to cross-docking. 14 out of 95 crystal structures exhibited docking accuracy for greater than 70% of ligands at RMSD cut off 2Å in the cross- docking studies. These 14 crystal structures were selected for the second part of the study, which included validation using DUD sets and enrichment calculations. 8 out of 14 crystal structures possessed the enrichment factor of >10 at 1% of the ranked database. ROC-AUC, AUAC, RIE, and BEDROC were calculated for these 8 crystal structures. 2WXV produced maximum BEDROC (0.768, at α=8) and RIE (11.22). 2WXV as a single initial crystal structure in the virtual screening protocol is likely to produce more accurate results than any other single crystal structure.

scholarly journals Lessons in Molecular Recognition:  The Effects of Ligand and Protein Flexibility on Molecular Docking Accuracy

2004 ◽  
Vol 47 (1) ◽  
pp. 45-55 ◽  
Author(s):  
Jon A. Erickson ◽  
Mehran Jalaie ◽  
Daniel H. Robertson ◽  
Richard A. Lewis ◽  
Michal Vieth
Keyword(s):  
Molecular Docking ◽  
Molecular Recognition ◽  
Protein Flexibility ◽  
Docking Accuracy

scholarly journals Multi-Body Interactions in Molecular Docking Program Devised with Key Water Molecules in Protein Binding Sites

Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2321 ◽  
Author(s):  
Wei Xiao ◽  
Disha Wang ◽  
Zihao Shen ◽  
Shiliang Li ◽  
Honglin Li
Keyword(s):  
The Other ◽  
Water Molecules ◽  
Protein Targets ◽  
Docking Simulations ◽  
Cross Docking ◽  
Docking Program ◽  
Screening Efficiency ◽  
Multi Body ◽  
Docking Accuracy ◽  
Length Optimization

Water molecules play an important role in modeling protein-ligand interactions. However, traditional molecular docking methods often ignore the impact of the water molecules by removing them without any analysis or keeping them as a static part of the proteins or the ligands. Hence, the accuracy of the docking simulations will inevitably be damaged. Here, we introduce a multi-body docking program which incorporates the fixed or the variable number of the key water molecules in protein-ligand docking simulations. The program employed NSGA II, a multi-objective optimization algorithm, to identify the binding poses of the ligand and the key water molecules for a protein. To this end, a force-field-based hydration-specific scoring function was designed to favor estimate the binding affinity considering the key water molecules. The program was evaluated in aspects of the docking accuracy, cross-docking accuracy, and screening efficiency. When the numbers of the key water molecules were treated as fixed-length optimization variables, the docking accuracy of the multi-body docking program achieved a success rate of 80.58% for the best RMSD values for the recruit of the ligands smaller than 2.0 Å. The cross-docking accuracy was investigated on the presence and absence of the key water molecules by four protein targets. The screening efficiency was assessed against those protein targets. Results indicated that the proposed multi-body docking program was with good performance compared with the other programs. On the other side, when the numbers of the key water molecules were treated as variable-length optimization variables, the program obtained comparative performance under the same three evaluation criterions. These results indicated that the multi-body docking with the variable numbers of the water molecules was also efficient. Above all, the multi-body docking program developed in this study was capable of dealing with the problem of the water molecules that explicitly participating in protein-ligand binding.

A Three-Dimensional Tetraphenylethylene-Based Fluorescence Covalent Organic Framework for Molecular Recognition

2020 ◽  
Author(s):  
Junxia Ren ◽  
Yaozu Liu ◽  
Xin Zhu ◽  
Yangyang Pan ◽  
Yujie Wang ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Fluorescence Probe ◽  
Three Dimensional ◽  
Hazardous Substances ◽  
Covalent Organic Framework ◽  
Highly Sensitive ◽  
Volatile Organic ◽  
Polycyclic Aromatic ◽  
Better Than ◽  
Organic Framework

<p><a></a><a></a><a></a><a></a><a></a><a></a><a></a><a>The development of highly-sensitive recognition of </a><a></a><a></a><a></a><a></a><a>hazardous </a>chemicals, such as volatile organic compounds (VOCs) and polycyclic aromatic hydrocarbons (PAHs), is of significant importance because of their widespread social concerns related to environment and human health. Here, we report a three-dimensional (3D) covalent organic framework (COF, termed JUC-555) bearing tetraphenylethylene (TPE) side chains as an aggregation-induced emission (AIE) fluorescence probe for sensitive molecular recognition.<a></a><a> </a>Due to the rotational restriction of TPE rotors in highly interpenetrated framework after inclusion of dimethylformamide (DMF), JUC-555 shows impressive AIE-based strong fluorescence. Meanwhile, owing to the large pore size (11.4 Å) and suitable intermolecular distance of aligned TPE (7.2 Å) in JUC-555, the obtained material demonstrates an excellent performance in the molecular recognition of hazardous chemicals, e.g., nitroaromatic explosives, PAHs, and even thiophene compounds, via a fluorescent quenching mechanism. The quenching constant (<i>K</i><sub>SV</sub>) is two orders of magnitude better than those of other fluorescence-based porous materials reported to date. This research thus opens 3D functionalized COFs as a promising identification tool for environmentally hazardous substances.</p>

Biomimetic Extracellular Vesicles Embedded with Black Phosphorus for Molecular Recognition-Guided Biomineralization

2018 ◽  
Author(s):  
Yingqian Wang ◽  
Xiaoxia Hu ◽  
Lingling Zhang ◽  
Chunli Zhu ◽  
Jie Wang ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Extracellular Vesicles ◽  
Inorganic Phosphate ◽  
Physiological Activity ◽  
Medical Engineering ◽  
Matrix Vesicles ◽  
Black Phosphorus ◽  
Photothermal Effect ◽  
Biological Processes ◽  
Extracellular Environment

Extracellular vesicles (EVs) are involved in the regulation of cell physiological activity and the reconstruction of extracellular environment. Matrix vesicles (MVs) are a type of EVs, and they participate in the regulation of cell mineralization. Herein, bioinspired MVs embedded with black phosphorus are functionalized with cell-specific aptamer (denoted as Apt-bioinspired MVs) for stimulating biomineralization. The aptamer can direct bioinspired MVs to targeted cells, and the increasing concentration of inorganic phosphate originated from the black phosphorus can facilitate cell biomineralization. The photothermal effect of the Apt-bioinspired MVs also positively affects mineralization. In addition, the Apt-bioinspired MVs display outstanding bone regeneration performance. Considering the excellent behavior of the Apt-bioinspired MVs for promoting biomineralization, our strategy provides a way of designing bionic tools for studying the mechanisms of biological processes and advancing the development of medical engineering.<br>

Arylboronic Acids in Self-condensation of Glucosamines Forming Deoxyfructosazine, Catalysts or Reagents?

2019 ◽  
Author(s):  
Meifeng Wang ◽  
Gan Zhu ◽  
Yiqun Li ◽  
Liuqun Gu
Keyword(s):  
Molecular Recognition ◽  
Boric Acid ◽  
Boronic Acid ◽  
Catalytic Mechanism ◽  
Organic Transformations ◽  
Food Industries ◽  
Arylboronic Acids ◽  
Excess Amount ◽  
Phenyl Boronic Acid ◽  
Boron Acid

Arylboronic acids were widely used as efficient catalysts in direct amide formation and other organic transformations. Surprisingly, reports on their use as catalysts in carbohydrates synthesis are very rare even though boron acid-diol complexation was extensively investigated in molecular recognition for saccharides and so on. Here we developed an efficient arylboronic acids catalyzed dimerization of glucosamines forming deoxyfructosazine which is important compound in pharmaceutical and food industries, against a commonly held belief that excess amount of phenyl boronic acid (or boric acid) is a must. A catalytic mechanism was also proposed and arylboronic acids instead of their boronates was identified as catalysts.

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