Insight 2 program

Manufactured by Dassault Systèmes

Sourced in United States

INSIGHT II is a program developed by Dassault Systèmes that provides a comprehensive set of tools for analyzing and visualizing scientific data. The program is designed to work with a variety of laboratory equipment and can be used to process, analyze, and interpret data collected from various experimental setups.

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Lab products found in correlation

Discover algorithm, by Dassault Systèmes (1 mentions)

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Insight II (22 citations)

4 protocols using insight 2 program

Structural Determination of Biomolecules via NMR

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The NOE-based
distance restraints
were obtained from NOESY spectra collected with a mixing time of 100
ms. The NOE cross-peaks were integrated with the XEASY program and
were converted into upper distance bounds using the CALIBA program
incorporated into the program package CYANA.^{92 (link)} Only NOE-derived constraints were considered in the annealing procedures.
An ensemble of 200 structures was generated with the simulated annealing
of the program CYANA. Then, 20 structures were chosen, whose interproton
distances best fitted NOE-derived distances, and refined through successive
steps of restrained and unrestrained energy minimization calculations
using the Discover algorithm (Accelrys, San Diego, CA) and the consistent
valence force field.^{93 (link)} The minimization
lowered the total energy of the structures; no residue was found in
the disallowed region of the Ramachandran plot. The final structures
were analyzed using the InsightII program (Accelrys, San Diego, CA).
Molecular graphics images were realized using the UCSF Chimera package.^{94 (link)}

Bellavita R., Casciaro B., Di Maro S., Brancaccio D., Carotenuto A., Falanga A., Cappiello F., Buommino E., Galdiero S., Novellino E., Grossmann T.N., Mangoni M.L., Merlino F, & Grieco P. (2021). First-in-Class Cyclic Temporin L Analogue: Design, Synthesis, and Antimicrobial Assessment. Journal of Medicinal Chemistry, 64(15), 11675-11694.

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Structural Analysis using AMBER 9

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The PTRAJ module of AMBER 9 was employed for structural analyses. The INSIGHTII program (Accelrys Software, Inc.) was employed for visualizing and model building. The figures and movies were prepared with Pymol [32 ].

Liu Z., Ding S., Kropachev K., Lei J., Amin S., Broyde S, & Geacintov N.E. (2015). Resistance to Nucleotide Excision Repair of Bulky Guanine Adducts Opposite Abasic Sites in DNA Duplexes and Relationships between Structure and Function. PLoS ONE, 10(9), e0137124.

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Structural Modeling of Ras Superfamily

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For the main body, except for N-terminal 34 amino acids, three x-ray crystal structures from the Ras superfamily were used as a template structure: human Rap1A (Protein Data Bank code: 1GUA), Rap2A (3RAP) and H-Ras (1K8R) structures. However, for the N-terminal domain, only one NMR structure was available: human interleukin-6 (1IL6). For homology-modelling procedures, the MODELER module in the INSIGHT II program (Accelrys, Inc., San Diego, CA, USA) was used to manipulate sequence and structure and to perform the calculations.

Rho S.B., Lee K.W., Lee S.H., Byun H.J., Kim B.R, & Lee C.H. (2021). Novel Anti-Angiogenic and Anti-Tumour Activities of the N-Terminal Domain of NOEY2 via Binding to VEGFR-2 in Ovarian Cancer. Biomolecules & Therapeutics, 29(5), 506-518.

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Conformational Analysis of TBA-F4 and TBA-F13 G-Quadruplexes

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The main conformational features of quadruplex adopted by TBA-F4 and TBA-F13 were explored by means of a molecular modelling study. The CFF91 force field using CFF91 atom types set was used (31 ,32 ). The initial coordinates for the starting model of TBA-F4 and TBA-F13 were taken from the NMR solution structure of the quadruplex d(GGTTGGTGTGGTTGG) (Protein Data Bank entry number 148D), with the first and best representative conformer of the twelve available ones submitted by Feigon etal. (33 (link)) The initial d(GGTFGGTGTGGTTGG) (TBA-F4) and d(GGTTGGTGTGGTFGG) (TBA-F13) G-quadruplex models were built by replacing the 5-methyl group of the thymine in the fourth and thirteenth position with a fluorine, using the Biopolymer building tool of Discover. The calculations were performed using a distance-dependent macroscopic dielectric constant of 4r and an infinite cut-off for non-bonded interactions to partially compensate for the lack of solvent used (34 ). Using steepest descent and conjugate gradient methods, the conformational energy of the complexes was minimized until convergence to an Root Mean Square (RMS) gradient of 0.1 kcal/mol Å was reached. Illustrations of the structure were generated using the INSIGHT II program, version 2005 (Accelrys, San Diego, CA, USA). All the calculations were performed on a PC running Linux ES 2.6.9.

Virgilio A., Petraccone L., Vellecco V., Bucci M., Varra M., Irace C., Santamaria R., Pepe A., Mayol L., Esposito V, & Galeone A. (2015). Site-specific replacement of the thymine methyl group by fluorine in thrombin binding aptamer significantly improves structural stability and anticoagulant activity. Nucleic Acids Research, 43(22), 10602-10611.

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