Journal ArticleDOI
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
Daniel R. Roe,Thomas E. Cheatham +1 more
TLDR
PTRAJ and its successor CPPTRAJ are described, two complementary, portable, and freely available computer programs for the analysis and processing of time series of three-dimensional atomic positions and the data therein derived.Abstract:
We describe PTRAJ and its successor CPPTRAJ, two complementary, portable, and freely available computer programs for the analysis and processing of time series of three-dimensional atomic positions (i.e., coordinate trajectories) and the data therein derived. Common tools include the ability to manipulate the data to convert among trajectory formats, process groups of trajectories generated with ensemble methods (e.g., replica exchange molecular dynamics), image with periodic boundary conditions, create average structures, strip subsets of the system, and perform calculations such as RMS fitting, measuring distances, B-factors, radii of gyration, radial distribution functions, and time correlations, among other actions and analyses. Both the PTRAJ and CPPTRAJ programs and source code are freely available under the GNU General Public License version 3 and are currently distributed within the AmberTools 12 suite of support programs that make up part of the Amber package of computer programs (see http://ambe...read more
Citations
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Journal ArticleDOI
The Effect of Force-Field Parameters on Cytochrome P450-Membrane Interactions: Structure and Dynamics.
Ghulam Mustafa,Prajwal P. Nandekar,Prajwal P. Nandekar,Prajwal P. Nandekar,Goutam Dev Mukherjee,Goutam Dev Mukherjee,Neil J. Bruce,Rebecca C. Wade,Rebecca C. Wade,Rebecca C. Wade +9 more
TL;DR: Comparison of the structural and dynamic properties of the proteins, the lipids and the protein-membrane interactions shows differing sensitivity of the cytochrome P450 isoforms to the choice of force field, with generally better agreement with experiment for the LIPID14 + ff14SB combination.
Journal ArticleDOI
Computational Study of the Driving Forces and Dynamics of Curcumin Binding to Amyloid-β Protofibrils
TL;DR: This work uses all-atom molecular dynamics simulations to study the dynamics and energetics of curcumin binding to an Aβ protofibril composed of 24 peptides, and shows thatCurcumin binds to specific hydrophobic sites on the prot ofibril surface and that binding is generally associated with the concomitant complexation of cur cumin into dimers, trimers, or tetramers.
Journal ArticleDOI
Coevolution of Eukaryote-like Vps4 and ESCRT-III Subunits in the Asgard Archaea.
Zhongyi Lu,Ting Fu,Ting Fu,Tianyi Li,Tianyi Li,Yang Liu,Siyu Zhang,Jinquan Li,Junbiao Dai,Junbiao Dai,Eugene V. Koonin,Guohui Li,Huiying Chu,Meng Li +13 more
TL;DR: Evidence is provided that the ESCRT complexes from Asgard archaea and eukaryotes are evolutionarily related and functionally similar, suggesting that despite the apparent absence of endomembranes in archaea, Eukaryotic ESCRT was inherited from an Asgard archaeal ancestor, alongside the emergence of endOMembrane system during eUKaryogenesis.
Journal ArticleDOI
New 19-Residue Peptaibols from Trichoderma Clade Viride
Tamás Marik,Chetna Tyagi,Gordana Racić,Dávid Rakk,András Szekeres,Csaba Vágvölgyi,László Kredics +6 more
TL;DR: In this article, the peptaibiomes of T. koningiopsis and T. gamsii were investigated by HPLC-ESI-MS, and the results revealed characteristic differences in bioactivities towards the different groups of target microorganisms, which can be explained with the differences in their cell wall structures.
Journal ArticleDOI
Revealing the atomistic details behind the binding of B7-1 to CD28 and CTLA-4: A comprehensive protein-protein modelling study.
TL;DR: This work employed a combination of advanced molecular modelling and extensive molecular dynamics simulations to model the CD28/B7-1 complex and characterize the key interactions that stabilize the complex, revealing the unique fingerprint hot-spot sites in CTLA-4/B 7-1 and CD28-1 complexes.
References
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