scholarly journals Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework

2019 ◽  
Vol 150 (22) ◽  
pp. 220901 ◽  
Author(s):  
Michael B. O’Connor ◽  
Simon J. Bennie ◽  
Helen M. Deeks ◽  
Alexander Jamieson-Binnie ◽  
Alex J. Jones ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Virtual Reality ◽  
Quantum Chemistry ◽  
Open Source ◽  
Drug Binding

scholarly journals Teaching Enzyme Catalysis Using an Open Source Framework for Interactive Molecular Dynamics in Virtual Reality

2019 ◽  
Author(s):  
Simon Bennie ◽  
Kara Ranaghan ◽  
Helen Deeks ◽  
Heather Goldsmith ◽  
Mike O'Connor ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Virtual Reality ◽  
Open Source ◽  
Molecular Mechanics ◽  
Real Time ◽  
Density Functional ◽  
Traditional Approach ◽  
Chorismate Mutase ◽  
Functional Theory

<div> <div> <p>The reemergence of virtual reality (VR) in the last few years has led to affordable commodity hardware that can offer new ways to teach, communicate and engage with difficult concepts, especially those which involve complicated 3D motion and spatial manipulation. In a higher education context, these immersive technologies make it possible to teach complex molecular topics in a way that may aid or even supersede traditional approaches such as molecular models, textbook images, and traditional screen-based computational environments. In this work we describe a study involving 24 third-year UK undergraduate chemistry students who undertook a traditional computational chemistry class complemented with an additional component utilising real-time interactive molecular dynamics simulations in VR (iMD-VR). Exploiting the flexibility of an open-source iMD-VR framework which we recently described,(1) and building on recent work where we demonstrated the ability to use this framework to run ‘on-the-fly’ density functional theory in VR at interactive speeds,2 we designed three tasks for students to complete in iMD-VR: (1) interactive rearrangement of the chorismate molecule to prephenate using forces obtained from ‘on-the-fly’ density functional theory calculations; (2) unbinding of chorismate from the active site chorismate mutase enzyme using molecular-mechanics forces calculated in real-time; and (3) docking of chorismate with chorismate mutase using real-time molecular mechanics forces. A survey indicated that most students found the iMD-VR component more engaging than the traditional approach, and also that it improved their perceived educational outcomes and their interest in continuing on in the field of computational sciences. </p></div> </div>

scholarly journals Teaching Enzyme Catalysis Using an Open Source Framework for Interactive Molecular Dynamics in Virtual Reality

2019 ◽  
Author(s):  
Simon Bennie ◽  
Kara Ranaghan ◽  
Helen Deeks ◽  
Heather Goldsmith ◽  
Mike O'Connor ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Virtual Reality ◽  
Open Source ◽  
Molecular Mechanics ◽  
Real Time ◽  
Density Functional ◽  
Traditional Approach ◽  
Chorismate Mutase ◽  
Functional Theory

<div> <div> <p>The reemergence of virtual reality (VR) in the last few years has led to affordable commodity hardware that can offer new ways to teach, communicate and engage with difficult concepts, especially those which involve complicated 3D motion and spatial manipulation. In a higher education context, these immersive technologies make it possible to teach complex molecular topics in a way that may aid or even supersede traditional approaches such as molecular models, textbook images, and traditional screen-based computational environments. In this work we describe a study involving 24 third-year UK undergraduate chemistry students who undertook a traditional computational chemistry class complemented with an additional component utilising real-time interactive molecular dynamics simulations in VR (iMD-VR). Exploiting the flexibility of an open-source iMD-VR framework which we recently described,(1) and building on recent work where we demonstrated the ability to use this framework to run ‘on-the-fly’ density functional theory in VR at interactive speeds,2 we designed three tasks for students to complete in iMD-VR: (1) interactive rearrangement of the chorismate molecule to prephenate using forces obtained from ‘on-the-fly’ density functional theory calculations; (2) unbinding of chorismate from the active site chorismate mutase enzyme using molecular-mechanics forces calculated in real-time; and (3) docking of chorismate with chorismate mutase using real-time molecular mechanics forces. A survey indicated that most students found the iMD-VR component more engaging than the traditional approach, and also that it improved their perceived educational outcomes and their interest in continuing on in the field of computational sciences. </p></div> </div>

Use of Molecular Dynamics Simulations in Structure-Based Drug Discovery

2019 ◽  
Vol 25 (31) ◽  
pp. 3339-3349 ◽  
Author(s):  
Indrani Bera ◽  
Pavan V. Payghan
Keyword(s):  
Molecular Dynamics ◽  
Drug Discovery ◽  
Molecular Dynamics Simulations ◽  
Drug Target ◽  
Structural Information ◽  
Drug Binding ◽  
Structure Based Drug Design ◽  
Drug Designing ◽  
Target Binding ◽  
Dynamics Simulations

Background: Traditional drug discovery is a lengthy process which involves a huge amount of resources. Modern-day drug discovers various multidisciplinary approaches amongst which, computational ligand and structure-based drug designing methods contribute significantly. Structure-based drug designing techniques require the knowledge of structural information of drug target and drug-target complexes. Proper understanding of drug-target binding requires the flexibility of both ligand and receptor to be incorporated. Molecular docking refers to the static picture of the drug-target complex(es). Molecular dynamics, on the other hand, introduces flexibility to understand the drug binding process. Objective: The aim of the present study is to provide a systematic review on the usage of molecular dynamics simulations to aid the process of structure-based drug design. Method: This review discussed findings from various research articles and review papers on the use of molecular dynamics in drug discovery. All efforts highlight the practical grounds for which molecular dynamics simulations are used in drug designing program. In summary, various aspects of the use of molecular dynamics simulations that underline the basis of studying drug-target complexes were thoroughly explained. Results: This review is the result of reviewing more than a hundred papers. It summarizes various problems that use molecular dynamics simulations. Conclusion: The findings of this review highlight how molecular dynamics simulations have been successfully implemented to study the structure-function details of specific drug-target complexes. It also identifies the key areas such as stability of drug-target complexes, ligand binding kinetics and identification of allosteric sites which have been elucidated using molecular dynamics simulations.

scholarly journals Qualitative Prediction of Ligand Dissociation Kinetics from Focal Adhesion Kinase Using Steered Molecular Dynamics

Life ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 74
Author(s):  
Justin Spiriti ◽  
Chung F. Wong
Keyword(s):  
Molecular Dynamics ◽  
Drug Discovery ◽  
Focal Adhesion Kinase ◽  
Focal Adhesion ◽  
Early Stage ◽  
Steered Molecular Dynamics ◽  
Drug Binding ◽  
Binding Kinetics ◽  
Dissociation Kinetics ◽  
Binding Characteristics

Most early-stage drug discovery projects focus on equilibrium binding affinity to the target alongside selectivity and other pharmaceutical properties. Since many approved drugs have nonequilibrium binding characteristics, there has been increasing interest in optimizing binding kinetics early in the drug discovery process. As focal adhesion kinase (FAK) is an important drug target, we examine whether steered molecular dynamics (SMD) can be useful for identifying drug candidates with the desired drug-binding kinetics. In simulating the dissociation of 14 ligands from FAK, we find an empirical power–law relationship between the simulated time needed for ligand unbinding and the experimental rate constant for dissociation, with a strong correlation depending on the SMD force used. To improve predictions, we further develop regression models connecting experimental dissociation rate with various structural and energetic quantities derived from the simulations. These models can be used to predict dissociation rates from FAK for related compounds.

Conformations of 2,4-Diphenylpentane:  A Quantum Chemistry and Gas-Phase Molecular Dynamics Simulation Study

1998 ◽  
Vol 102 (24) ◽  
pp. 4694-4702 ◽  
Author(s):  
Grant D. Smith ◽  
Chakravarthy Ayyagari ◽  
Richard L. Jaffe ◽  
Matthew Pekny ◽  
Aaron Bernarbo
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Quantum Chemistry ◽  
Gas Phase ◽  
Simulation Study ◽  
Dynamics Simulation

scholarly journals Psi4 1.4: Open-Source Software for High-Throughput Quantum Chemistry

2020 ◽  
Author(s):  
Daniel Smith ◽  
Lori Burns ◽  
Andrew Simmonett ◽  
Robert Parrish ◽  
Matthew Schieber ◽  
...  
Keyword(s):  
Perturbation Theory ◽  
Quantum Chemistry ◽  
Open Source ◽  
Density Functional ◽  
Many Body ◽  
Hartree Fock ◽  
Large Numbers ◽  
Many Body Perturbation Theory ◽  
Infrastructure Project ◽  
Job Specification

<div> <div> <div> <p>Psi4 is a free and open-source ab initio electronic structure program providing Hartree–Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Python API, facilitating post-processing and complex workflows; method developers also have access to most of Psi4’s core functionality via Python. Job specification may be passed using The Molecular Sciences Software Institute (MolSSI) QCSchema data format, facilitating interoperability. A rewrite of our top-level computation driver, and concomitant adoption of the MolSSI QCArchive Infrastructure project, make the latest version of Psi4 well suited to distributed computation of large numbers of independent tasks. The project has fostered the development of independent software components that may be reused in other quantum chemistry programs. </p> </div> </div> </div>

scholarly journals ACE-Molecule: An open-source real-space quantum chemistry package

2020 ◽  
Vol 152 (12) ◽  
pp. 124110 ◽  
Author(s):  
Sungwoo Kang ◽  
Jeheon Woo ◽  
Jaewook Kim ◽  
Hyeonsu Kim ◽  
Yongjun Kim ◽  
...  
Keyword(s):  
Quantum Chemistry ◽  
Open Source ◽  
Real Space
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