Predictive Power of Different Types of Experimental Restraints in Small Molecule Docking: A Review

2018 ◽  
Vol 58 (2) ◽  
pp. 225-233 ◽  
Author(s):  
Darwin Y. Fu ◽  
Jens Meiler
Keyword(s):  
Small Molecule ◽  
Predictive Power ◽  
Different Types ◽  
Molecule Docking

scholarly journals Competition NMR for Detection of Hit/Lead Inhibitors of Protein–Protein Interactions

Molecules ◽  
2020 ◽  
Vol 25 (13) ◽  
pp. 3017 ◽  
Author(s):  
Bogdan Musielak ◽  
Weronika Janczyk ◽  
Ismael Rodriguez ◽  
Jacek Plewka ◽  
Dominik Sala ◽  
...  
Keyword(s):  
Small Molecule ◽  
Protein Interactions ◽  
Point Mutations ◽  
Protein Protein Interactions ◽  
Competition Assay ◽  
Fragment Screening ◽  
Different Types ◽  
Lead Inhibitors

Screening for small-molecule fragments that can lead to potent inhibitors of protein–protein interactions (PPIs) is often a laborious step as the fragments cannot dissociate the targeted PPI due to their low μM–mM affinities. Here, we describe an NMR competition assay called w-AIDA-NMR (weak-antagonist induced dissociation assay-NMR), which is sensitive to weak μM–mM ligand–protein interactions and which can be used in initial fragment screening campaigns. By introducing point mutations in the complex’s protein that is not targeted by the inhibitor, we lower the effective affinity of the complex, allowing for short fragments to dissociate the complex. We illustrate the method with the compounds that block the Mdm2/X-p53 and PD-1/PD-L1 oncogenic interactions. Targeting the PD-/PD-L1 PPI has profoundly advanced the treatment of different types of cancers.

scholarly journals Tailoring the specificity of the type C feruloyl esterase FoFaeC from Fusarium oxysporum towards methyl sinapate by rational redesign based on small molecule docking simulations

PLoS ONE ◽  
2018 ◽  
Vol 13 (5) ◽  
pp. e0198127 ◽  
Author(s):  
Io Antonopoulou ◽  
Cameron Hunt ◽  
Gabriella Cerullo ◽  
Simona Varriale ◽  
Alexandra Gerogianni ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Small Molecule ◽  
Feruloyl Esterase ◽  
Docking Simulations ◽  
Type C ◽  
Molecule Docking

Predicting matches in international football tournaments with random forests

2018 ◽  
Vol 18 (5-6) ◽  
pp. 460-482 ◽  
Author(s):  
Gunther Schauberger ◽  
Andreas Groll
Keyword(s):  
Random Forests ◽  
Statistical Models ◽  
Regression Models ◽  
Predictive Power ◽  
Statistical Modelling ◽  
World Cup ◽  
Fifa World Cup ◽  
Specific Data ◽  
Covariate Information ◽  
Different Types

Many approaches that analyse and predict results of international matches in football are based on statistical models incorporating several potentially influential covariates with respect to a national team's success, such as the bookmakers’ ratings or the FIFA ranking. Based on all matches from the four previous FIFA World Cups 2002–2014, we compare the most common regression models that are based on the teams’ covariate information with regard to their predictive performances with an alternative modelling class, the so-called random forests. Random forests can be seen as a mixture between machine learning and statistical modelling and are known for their high predictive power. Here, we consider two different types of random forests depending on the choice of response. One type of random forests predicts the precise numbers of goals, while the other type considers the three match outcomes—win, draw and loss—using special algorithms for ordinal responses. To account for the specific data structure of football matches, in particular at FIFA World Cups, the random forest methods are slightly altered compared to their standard versions and adapted to the specific needs of the application to FIFA World Cup data.

Correction to On the Applicability of Elastic Network Normal Modes in Small-Molecule Docking

2014 ◽  
Vol 54 (12) ◽  
pp. 3453-3453 ◽  
Author(s):  
Matthias Dietzen ◽  
Elena Zotenko ◽  
Andreas Hildebrandt ◽  
Thomas Lengauer
Keyword(s):  
Small Molecule ◽  
Normal Modes ◽  
Elastic Network ◽  
Molecule Docking

scholarly journals Full Assignment of Ab-Initio Raman Spectra at Finite Temperatures Using Wannier Polarizabilities: Application to Cyclohexane Molecule in Gas Phase

Micromachines ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1212
Author(s):  
Pouya Partovi-Azar ◽  
Thomas Kühne
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Gas Phase ◽  
Raman Spectra ◽  
Predictive Power ◽  
Ab Initio Molecular Dynamics ◽  
Spatial Spread ◽  
Wannier Functions ◽  
Different Types ◽  
Cross Correlations

We demonstrate how to fully ascribe Raman peaks simulated using ab initio molecular dynamics to specific vibrations in the structure at finite temperatures by means of Wannier functions. Here, we adopt our newly introduced method for the simulation of the Raman spectra in which the total polarizability of the system is expressed as a sum over Wannier polarizabilities. The assignment is then based on the calculation of partial Raman activities arising from self- and/or cross-correlations between different types of Wannier functions in the system. Different types of Wannier functions can be distinguished based on their spatial spread. To demonstrate the predictive power of this approach, we applied it to the case of a cyclohexane molecule in the gas phase and were able to fully assign the simulated Raman peaks.

scholarly journals Varying experimental conditions to study interactions in the solid state

2014 ◽  
Vol 70 (a1) ◽  
pp. C631-C631
Author(s):  
Elena Boldyreva
Keyword(s):  
Crystal Structure ◽  
Solid State ◽  
Crystal Structures ◽  
Intermolecular Interactions ◽  
Small Molecule ◽  
Variable Temperature ◽  
Variable Pressure ◽  
Continuous Lattice ◽  
Experimental Conditions ◽  
Different Types

Supramolecular interactions in the solid state attract much attention. Different experimental and computational approaches are used, to predict and to design crystal structures, to predict the properties based on molecular and crystal structures, to range different types of intermolecular interactions. Analysis of the crystal structures at fixed (e.g. ambient) temperature and pressure conditions is most common for experiments, whereas most DFT calculations are limited to 0 K, to minimize computational costs. At the same time, evolution of a crystal structure as a function of experimental conditions can contribute significantly to understanding the structure-forming role and relative energies of different types of intermolecular interactions in the same crystal structure and of similar interactions in a series of different but structurally or chemically related compounds. In the present invited contribution I attempt to illustrate this using several selected examples from my own practice and from the papers published by other research groups. I consider, in particular, the results of variable-temperature and variable-pressure studies of continuous lattice strain and phase transitions in small-molecule organic compounds, the results of variable-temperature and variable-pressure crystallization, the results of comparing the dissolution profiles of mono- and multi-component small-molecule organic crystals. I shall also discuss how variable-temperature and variable-pressure experimental diffraction data can assist in optimizing the calculations aimed at comparing the relative stability of polymorphs and predicting polymorph transitions. The study was supported by Russian Ministry of Science and Education and Russian Academy of Sciences.

From slow to fast – the user controls the rate of the release of molecules from masked forms using a photoswitch and different types of light

2015 ◽  
Vol 51 (32) ◽  
pp. 7039-7042 ◽  
Author(s):  
C. Chad Warford ◽  
Carl-Johan Carling ◽  
Neil R. Branda
Keyword(s):  
Visible Light ◽  
Small Molecule ◽  
Different Types

Light-gated release of a small molecule increases when exposed to UV or visible light.

Sign in / Sign up

Export Citation Format

Share Document