Computational Modelling of Constructive Interaction: Relaxing the Mutuality Hypothesis

Host-guest binding remains a major challenge in modern computational modelling. The newest 7<sup>th</sup> statistical assessment of the modeling of proteins and ligands (SAMPL) challenge contains a new series of host-guest systems. The TrimerTrip host binds to 16 structurally diverse guests. Previously, we have successfully employed the spherical coordinates as the collective variables coupled with the enhanced sampling technique metadynamics to enhance the sampling of the binding/unbinding event, search for possible binding poses and predict the binding affinities in all three host-guest binding cases of the 6<sup>th</sup> SAMPL challenge. In this work, we employed the same protocol to investigate the TrimerTrip host in the SAMPL7 challenge. As no binding pose is provided by the SAMPL7 host, our simulations initiate from randomly selected configurations and are proceeded long enough to obtain converged free energy estimates and search for possible binding poses. The predicted binding affinities are in good agreement with the experimental reference, and the obtained binding poses serve as a nice starting point for end-point or alchemical free energy calculations.

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Computational Modelling in Studies for Hepatitis C Virus (HCV) NS3 Protease

Current Topics in Medicinal Chemistry ◽

10.2174/1568026616666151120112141 ◽

2016 ◽

Vol 16 (12) ◽

pp. 1351-1361

Author(s):

Azat Mukhametov

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Computational Modelling ◽

Ns3 Protease

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Pollutants in Organic Chemistry and Medicinal Chemistry Education Laboratory. Experimental and Machine Learning Studies

Current Topics in Medicinal Chemistry ◽

10.2174/1568026620666200211110043 ◽

2020 ◽

Vol 20 (9) ◽

pp. 720-730

Author(s):

Iker Montes-Bageneta ◽

Urtzi Akesolo ◽

Sara López ◽

Maria Merino ◽

Eneritz Anakabe ◽

...

Keyword(s):

Organic Chemistry ◽

Machine Learning ◽

Chemistry Education ◽

Organic Waste ◽

Computational Modelling ◽

University Education ◽

Academic Factors ◽

Academic Year ◽

Statistical Analysis Software

Aims: Computational modelling may help us to detect the more important factors governing this process in order to optimize it. Background: The generation of hazardous organic waste in teaching and research laboratories poses a big problem that universities have to manage. Methods: In this work, we report on the experimental measurement of waste generation on the chemical education laboratories within our department. We measured the waste generated in the teaching laboratories of the Organic Chemistry Department II (UPV/EHU), in the second semester of the 2017/2018 academic year. Likewise, to know the anthropogenic and social factors related to the generation of waste, a questionnaire has been utilized. We focused on all students of Experimentation in Organic Chemistry (EOC) and Organic Chemistry II (OC2) subjects. It helped us to know their prior knowledge about waste, awareness of the problem of separate organic waste and the correct use of the containers. These results, together with the volumetric data, have been analyzed with statistical analysis software. We obtained two Perturbation-Theory Machine Learning (PTML) models including chemical, operational, and academic factors. The dataset analyzed included 6050 cases of laboratory practices vs. practices of reference. Results: These models predict the values of acetone waste with R2 = 0.88 and non-halogenated waste with R2 = 0.91. Conclusion: This work opens a new gate to the implementation of more sustainable techniques and a circular economy with the aim of improving the quality of university education processes.

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MINGLED METAMORPHISM: COMPUTATIONAL MODELLING OF AN OXIDIZED FRANCISCAN BLUESCHIST-ECLOGITE AND IMPLICATIONS FOR METAMORPHIC EVOLUTIONARY MODELS

10.1130/abs/2016am-282106 ◽

2016 ◽

Author(s):

Andrea E. Goltz ◽

◽

F. Zeb Page

Keyword(s):

Computational Modelling ◽

Evolutionary Models

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Recycling and Reuse in the Roman Economy

10.1093/oso/9780198860846.001.0001 ◽

2020 ◽

Keyword(s):

Building Materials ◽

Computational Modelling ◽

Late Antique ◽

Roman Economy ◽

Wide Range ◽

The Status ◽

Recent Developments ◽

Methodological Approaches ◽

First Time ◽

Site Types

The recycling and reuse of materials and objects were extensive in the past, but have rarely been embedded into models of the economy; even more rarely has any attempt been made to assess the scale of these practices. Recent developments, including the use of large datasets, computational modelling, and high-resolution analytical chemistry, are increasingly offering the means to reconstruct recycling and reuse, and even to approach the thorny matter of quantification. Growing scholarly interest in the topic has also led to an increasing recognition of these practices from those employing more traditional methodological approaches, which are sometimes coupled with innovative archaeological theory. Thanks to these efforts, it has been possible for the first time in this volume to draw together archaeological case studies on the recycling and reuse of a wide range of materials, from papyri and textiles, to amphorae, metals and glass, building materials and statuary. Recycling and reuse occur at a range of site types, and often in contexts which cross-cut material categories, or move from one object category to another. The volume focuses principally on the Roman Imperial and late antique world, over a broad geographical span ranging from Britain to North Africa and the East Mediterranean. Last, but not least, the volume is unique in focusing upon these activities as a part of the status quo, and not just as a response to crisis.

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