Progress towards Automated Kepler Scientific Workflows for Computer-aided Drug Discovery and Molecular Simulations

Ieong, Pek U; Sørensen, Jesper Givskov; Vemu, Prasantha L.; Wong, Celia W.; Demir, Özlem; Williams, Nadya; Wang, Jianwu; Crawl, Daniel; Swift, Robert V.; Malmstrom, Robert D.; Altıntaş, Ilkay; Amaro, Rommie E.

doi:10.1016/j.procs.2014.05.159

Cited by 7 publications

(11 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Due to the countless options available in the configuration file of MD software reproducibility has been a key issue in MD simulations. Workflow management, already available as a tool external to MD software 59 , offers a solution by keeping a log of all steps taken. QwikMD, while guiding the user interactively through the process of preparing, running and analyzing MD simulations, keeps track of every single step by writing two files, a .qwikMD file and a .infoMD file.…”

Section: Methodsmentioning

confidence: 99%

QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts

Ribeiro

Bernardi

Rudack

et al. 2016

Sci Rep

191

160

View full text Add to dashboard Cite

The proper functioning of biomolecules in living cells requires them to assume particular structures and to undergo conformational changes. Both biomolecular structure and motion can be studied using a wide variety of techniques, but none offers the level of detail as do molecular dynamics (MD) simulations. Integrating two widely used modeling programs, namely NAMD and VMD, we have created a robust, user-friendly software, QwikMD, which enables novices and experts alike to address biomedically relevant questions, where often only molecular dynamics simulations can provide answers. Performing both simple and advanced MD simulations interactively, QwikMD automates as many steps as necessary for preparing, carrying out, and analyzing simulations while checking for common errors and enabling reproducibility. QwikMD meets also the needs of experts in the field, increasing the efficiency and quality of their work by carrying out tedious or repetitive tasks while enabling easy control of every step. Whether carrying out simulations within the live view mode on a small laptop or performing complex and large simulations on supercomputers or Cloud computers, QwikMD uses the same steps and user interface. QwikMD is freely available by download on group and personal computers. It is also available on the cloud at Amazon Web Services.

show abstract

Section: Methodsmentioning

confidence: 99%

QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts

Ribeiro

Bernardi

Rudack

et al. 2016

Sci Rep

191

160

View full text Add to dashboard Cite

show abstract

“…Currently, molecular simulation, which is based on investigation of the binding interaction mechanism of a biomacromolecule with small molecules, plays an important role in the discovery and development of drugs . In this work, molecular dockings between lovastatin and four B‐DNA fragments were performed using Autodock 4.2 to further clarify the binding mode of lovastatin with B‐DNA and to obtain information about the interaction forces.…”

Section: Resultsmentioning

confidence: 99%

Combined spectroscopic and molecular docking approach to probing binding interactions between lovastatin and calf thymus DNA

Chen

Wang

et al. 2015

Luminescence

View full text Add to dashboard Cite

The binding interaction of lovastatin with calf thymus DNA (ct-DNA) was studied using UV/Vis absorption spectroscopy, fluorescence emission spectroscopy, circular dichroism (CD), viscosity measurement and molecular docking methods. The experimental results showed that there was an obvious binding interaction of lovastatin with ct-DNA and the binding constant (Kb ) was 5.60 × 10(3) M(-1) at 298 K. In the binding process of lovastatin with ct-DNA, the enthalpy change (ΔH(0)) and entropy change (ΔS(0)) were -24.9 kJ/mol and -12.0 J/mol/K, respectively, indicating that the main binding interaction forces were van der Waal's force and hydrogen bonding. The molecular docking results suggested that lovastatin preferred to bind on the minor groove of different B-DNA fragments and the conformation change of lovastatin in the lovastatin-DNA complex was obviously observed, implying that the flexibility of lovastatin molecule plays an important role in the formation of the stable lovastatin-ct-DNA complex.

show abstract

“…This approach is practical and warranted in settings where the goal is to screen large libraries of potential drug compounds [ 189 – 191 ]. An extensive review of the unique challenges in these settings can be found in [ 163 , 192 ].…”

Section: Recent Applications Made Possible By Hardware and Algorithmimentioning

confidence: 99%

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics

et al. 2016

View full text Add to dashboard Cite

Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been made toward this end in silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics. This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of characterizing equilibrium structure and dynamics. In addition to surveying recent applications that showcase current capabilities of computational methods, this review highlights state-of-the-art algorithmic techniques proposed to overcome challenges posed in silico by the disparate spatial and time scales accessed by dynamic macromolecules. This review is not meant to be exhaustive, as such an endeavor is impossible, but rather aims to balance breadth and depth of strategies for modeling macromolecular structure and dynamics for a broad audience of novices and experts.

show abstract

Progress towards Automated Kepler Scientific Workflows for Computer-aided Drug Discovery and Molecular Simulations

Cited by 7 publications

References 32 publications

QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts

QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts

Combined spectroscopic and molecular docking approach to probing binding interactions between lovastatin and calf thymus DNA

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics

Contact Info

Product

Resources

About