Article Commentary: Graphical User Interfaces for Molecular Dynamics—Quo Vadis?

In the past years an increasing number of graphical user interfaces for Molecular Dynamics (MD) were presented and concomitantly, more and more Molecular Dynamics studies were published. With the easier application of MD software packages the field runs the risk however, of being pervaded with unreliable results. Therefore, possible benefits and caveats have to be carefully balanced. Here we outline in which respects a broader access of MD via graphical user interfaces may help to increase the usability of Molecular Dynamics simulations while maintaining their quality.

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Biochemical Characterization of IMP-30, a Metallo-β-Lactamase with Enhanced Activity toward Ceftazidime

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02341-12 ◽

2013 ◽

Vol 57 (10) ◽

pp. 5122-5126 ◽

Cited By ~ 6

Author(s):

Kevin M. Pegg ◽

Eleanor M. Liu ◽

Alecander E. LaCuran ◽

Peter Oelschlaeger

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Biochemical Characterization ◽

Water Access ◽

Important Family ◽

The Past ◽

Enhanced Activity ◽

Dynamics Simulations

ABSTRACTIMP-type enzymes constitute a clinically important family of metallo-β-lactamases that has grown dramatically in the past decade to its current 45 known members. Here, we report the biochemical characterization of IMP-30 in comparison to IMP-1, from which it deviates by a single E59K mutation. Kinetics, MIC assays, docking, and molecular dynamics simulations support a scenario in which Lys59 interacts with the ceftazidime R1group, resulting in increased water access and enhanced turnover and MIC of ceftazidime.

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Advances in Molecular Dynamics Simulations of Nanotribology

STLE/ASME 2008 International Joint Tribology Conference ◽

10.1115/ijtc2008-71201 ◽

2008 ◽

Author(s):

Michael Chandross

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

State Of The Art ◽

Simulation Method ◽

Detailed Understanding ◽

The Past ◽

Simulation Techniques ◽

Dynamics Simulations ◽

The Individual ◽

Made In

Molecular dynamics is the simulation method that is most amenable to the length and time scales of nanotribological experiments. The ability to track the individual motion of every atom in simulations has led to a detailed understanding of the underlying physics that is difficult to extract from experiment. While significant progress has been made in simulations over the past two decades, computational issues still limit the types of problems that can be approached, and the detailed understanding that results. Here we discuss recent advances in molecular dynamics simulations that push the bounds of simulation size, velocity, and chemistry. These state of the art simulation techniques have made great strides in allowing detailed comparisons to experimental results. These advances will be placed in context by addressing the barriers that remain and where future progress lies.

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