Journal ArticleDOI
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
Daniel R. Roe,Thomas E. Cheatham +1 more
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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
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Interference between Triplex and Protein Binding to Distal Sites on Supercoiled DNA.
TL;DR: It is observed that the interaction between the two ligands through their influence on their DNA template is determined by a subtle interplay of DNA mechanics and electrostatics, that the changes in flexibility induced by ligand binding play an important role and that supercoiling can instigate additional ligand-DNA contacts that would not be possible in simple linear DNA sequences.
Journal ArticleDOI
Host-Guest Interactions between Candesartan and Its Prodrug Candesartan Cilexetil in Complex with 2-Hydroxypropyl-β-cyclodextrin: On the Biological Potency for Angiotensin II Antagonism.
Dimitrios Ntountaniotis,Ioannis Andreadelis,Tahsin F. Kellici,Vlasios Karageorgos,Georgios Leonis,Eirini Christodoulou,Sofia Kiriakidi,Johanna Becker-Baldus,Evgenios K. Stylos,Maria V. Chatziathanasiadou,Christos M. Chatzigiannis,Dimitrios Damalas,Busecan Aksoydan,Uroš Javornik,Georgia Valsami,Clemens Glaubitz,Serdar Durdagi,Nikolaos S. Thomaidis,Antonios Kolocouris,Janez Plavec,Andreas G. Tzakos,George Liapakis,Thomas Mavromoustakos +22 more
TL;DR: It was shown that as a result of CAN's complexation, CAN exerts higher antagonistic activity than CC, and a formulation of CC with 2-HP-β-CD is not indicated, while the formulation with CAN is promising and needs further investigation.
Journal ArticleDOI
Probing the structure and in silico stability of cargo loaded DNA icosahedra using MD simulations
TL;DR: In this article, an atomistic model of a well-characterized DNA icosahedron, with demonstrated versatile functionalities in biological systems, is presented, where the major modes of internal motion have been identified using principal component analysis.
Journal ArticleDOI
α-Glucosidase inhibitors from brown rice bound phenolics extracts (BRBPE): Identification and mechanism
TL;DR: In this article , the α-glucosidase inhibitors in BRBPE were screened using bioaffinity ultra-filtration methods, and seven phenolic compounds - three monomers (p-coumaric acid, ferulic acid and methyl ferulate), three dimers (8-5, 5-5' and 8-O-4' diferulic acid) and a trimer (5-5'/8-O4″ dehydrotriferilic acid) were identified as exact inhibitors.
Journal ArticleDOI
Photogeneration of Quinone Methides as Latent Electrophiles for Lysine Targeting.
Raúl Pérez-Ruiz,Raúl Pérez-Ruiz,Oscar Molins-Molina,Emilio Lence,Concepción González-Bello,Miguel A. Miranda,M. Consuelo Jiménez +6 more
TL;DR: The utility of 4-trifluoromethyl phenols as precursors of latent electrophiles, quinone methides (QM), for lysine-targeting is demonstrated and the opportunity of performing protein silencing by generating reactive ligands under very mild conditions (irradiation) for specific covalent modification of hidden lysines residues is opened.
References
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VMD: Visual molecular dynamics
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Journal ArticleDOI
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
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The Amber biomolecular simulation programs
David A. Case,Thomas E. Cheatham,Tom Darden,Holger Gohlke,Ray Luo,Kenneth M. Merz,Alexey V. Onufriev,Carlos Simmerling,Bing Wang,Robert J. Woods +9 more
TL;DR: The development, current features, and some directions for future development of the Amber package of computer programs, which contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.
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General definition of ring puckering coordinates
Dieter Cremer,John A. Pople +1 more
TL;DR: In this article, a unique mean plane is defined for a general monocyclic puckered ring, which is described by amplitude and phase coordinates which are generalizations of those introduced for cyclopentane by Kilpatrick, Pitzer, and Spitzer.