Equilibrium molecular-pair treatment of fast bimolecular reactions in solution

1987 ◽  
pp. 1440
Author(s):  
John F. Garst
Keyword(s):  
Bimolecular Reactions ◽  
Molecular Pair

mmpdb: An Open Source Matched Molecular Pair Platform for Large Multi-Property Datasets

2018 ◽  
Author(s):  
Andrew Dalke ◽  
Jerome Hert ◽  
Christian Kramer
Keyword(s):  
Open Source ◽  
Large Datasets ◽  
Molecular Pair ◽  
New Algorithms

We present mmpdb, an open source Matched Molecular Pair (MMP) platform to create, compile, store, retrieve, and use MMP rules. mmpdb is suitable for the large datasets typically found in pharmaceutical and agrochemical companies and provides new algorithms for fragment canonicalization and stereochemistry handling. The platform is written in Python and based on the RDKit toolkit. mmpdb is freely available.

Bioactivity Prediction Based on Matched Molecular Pair and Matched Molecular Series Methods

2020 ◽  
Vol 26 (33) ◽  
pp. 4195-4205
Author(s):  
Xiaoyu Ding ◽  
Chen Cui ◽  
Dingyan Wang ◽  
Jihui Zhao ◽  
Mingyue Zheng ◽  
...  
Keyword(s):  
Prediction Model ◽  
Large Scale ◽  
Prediction Models ◽  
Predictive Accuracy ◽  
Lead Optimization ◽  
Consensus Method ◽  
Molecular Pair ◽  
Bioactivity Prediction ◽  
Compound Synthesis ◽  
Consensus Modeling

Background: Enhancing a compound’s biological activity is the central task for lead optimization in small molecules drug discovery. However, it is laborious to perform many iterative rounds of compound synthesis and bioactivity tests. To address the issue, it is highly demanding to develop high quality in silico bioactivity prediction approaches, to prioritize such more active compound derivatives and reduce the trial-and-error process. Methods: Two kinds of bioactivity prediction models based on a large-scale structure-activity relationship (SAR) database were constructed. The first one is based on the similarity of substituents and realized by matched molecular pair analysis, including SA, SA_BR, SR, and SR_BR. The second one is based on SAR transferability and realized by matched molecular series analysis, including Single MMS pair, Full MMS series, and Multi single MMS pairs. Moreover, we also defined the application domain of models by using the distance-based threshold. Results: Among seven individual models, Multi single MMS pairs bioactivity prediction model showed the best performance (R2 = 0.828, MAE = 0.406, RMSE = 0.591), and the baseline model (SA) produced the most lower prediction accuracy (R2 = 0.798, MAE = 0.446, RMSE = 0.637). The predictive accuracy could further be improved by consensus modeling (R2 = 0.842, MAE = 0.397 and RMSE = 0.563). Conclusion: An accurate prediction model for bioactivity was built with a consensus method, which was superior to all individual models. Our model should be a valuable tool for lead optimization.

Bimolecular Reactions, Transition-State Theory

2018 ◽  
Author(s):  
Niels Engholm Henriksen ◽  
Flemming Yssing Hansen
Keyword(s):  
Transition State ◽  
Saddle Point ◽  
Transition State Theory ◽  
Classical Mechanics ◽  
Small Degree ◽  
State Theory ◽  
Reaction Coordinate ◽  
Partition Functions ◽  
Bimolecular Reactions ◽  
Activated Complex

This chapter discusses an approximate approach—transition-state theory—to the calculation of rate constants for bimolecular reactions. A reaction coordinate is identified from a normal-mode coordinate analysis of the activated complex, that is, the supermolecule on the saddle-point of the potential energy surface. Motion along this coordinate is treated by classical mechanics and recrossings of the saddle point from the product to the reactant side are neglected, leading to the result of conventional transition-state theory expressed in terms of relevant partition functions. Various alternative derivations are presented. Corrections that incorporate quantum mechanical tunnelling along the reaction coordinate are described. Tunnelling through an Eckart barrier is discussed and the approximate Wigner tunnelling correction factor is derived in the limit of a small degree of tunnelling. It concludes with applications of transition-state theory to, for example, the F + H2 reaction, and comparisons with results based on quasi-classical mechanics as well as exact quantum mechanics.

Brownian dynamics simulation of diffusion‐influenced bimolecular reactions

1984 ◽  
Vol 80 (4) ◽  
pp. 1517-1524 ◽  
Author(s):  
Scott H. Northrup ◽  
Stuart A. Allison ◽  
J. Andrew McCammon
Keyword(s):  
Brownian Dynamics ◽  
Dynamics Simulation ◽  
Brownian Dynamics Simulation ◽  
Bimolecular Reactions
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