Insight 2

Manufactured by Dassault Systèmes

Sourced in United States

Insight II is a high-performance laboratory equipment product designed for scientific analysis and research. It provides advanced imaging and data acquisition capabilities to support various experimental and testing requirements in a laboratory environment.

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Lab products found in correlation

Discovery studio visualizer 4, by Dassault Systèmes (1 mentions) Plenti puro, by Addgene (1 mentions) Discover 2, by Dassault Systèmes (1 mentions) Discovery studio, by Dassault Systèmes (1 mentions)

Close spelling variants of this product

Insight II 2005 (7 citations) INSIGHT II program (4 citations) Insight II version 2000 (2 citations) Insight II/Discover ( (2 citations) Insight II software (2 citations)

22 protocols using insight 2

Molecular Modeling of Chicken IgY

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Molecular modelling of IgY was performed on a Silicon Graphics Fuel workstation using InsightII and Discover software (Accelrys Inc., San Diego, USA). Figures were produced using the program Pymol [18 ]. Protein structures used for modelling were obtained from the Protein Data Bank (PDB) database [19 (link)]. The peptide structure of chicken IgY was based on the crystal structures of human IgE domains Cε2–4[20 (link)] and human IgG Fab domain [21 (link)]. Sequence alignment and methods for generation of homology model are provided in S1 File.

Gilgunn S., Millán Martín S., Wormald M.R., Zapatero-Rodríguez J., Conroy P.J., O’Kennedy R.J., Rudd P.M, & Saldova R. (2016). Comprehensive N-Glycan Profiling of Avian Immunoglobulin Y. PLoS ONE, 11(7), e0159859.

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Structural Analysis of NC1 Hexamers

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Amino acid sequences were obtained from UniProt database. The color scheme used for alignments is from the algorithm in Clustal Omega and MView. Each amino acid is colored when it meets the criteria specific for the residue type. This analysis is conducted by Clustal X and viewed by Jalview. The 3D modeling of the structures of the [(α1)2(α2)]2 NC1 hexamers from human placenta basement membranes (Protein Data Bank ID 1LI1) were rendered using the molecular graphics visualization program YASARA (YASARA Bio-sciences) and analyzed to generate modeled structures using the molecular graphics software InsightII (Accelrys). Percentage of homology was calculated by multiplying the query coverage and percent identity of each comparison with usage of NCBI blast tool.

Ogilvy S., Metcalf D., Print C.G., Bath M.L., Harris A.W, & Adams J.M. (1999). Constitutive Bcl-2 expression throughout the hematopoietic compartment affects multiple lineages and enhances progenitor cell survival. Proceedings of the National Academy of Sciences of the United States of America, 96(26), 14943-14948.

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Modeling Oxime Interactions with Phosphonylated AChE

Cited 1 time

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Models of oximes RS-170B, HI-6 and RS-169A were prepared with Insight II (Accelrys, San Diego) as described earlier for HI-6 and similar imidazole oximes.^{17 (link),18 (link)} The crystal structure of soman-TcAChE conjugate (PDB id 2WFZ) was used as a source of phosphonylated active center serine, and was pasted into 3D structure of human AChE (PDB id 4EY4). All water molecules and reversibly bound ligands were removed, while incompletely resolved amino acid side-chains were repaired. Oximes were oriented into the soman-hAChE gorge with their oximate oxygens approx. 4 Å from the conjugated phosphorus atom. A flexible distance constraint was placed between those two atoms at 3 Å, and molecular dynamics (MD) calculations were performed as described before.^{18 (link)} Only selected hAChE side-chains (Y70, Y124, S203, W286, F295, F297, Y341 and H447) and the phosphonyl conjugate were allowed to rotate during simulation together with oxime. Ten calculations were performed per oxime. Resulting structures were visualized using Discovery Studio Visualizer 4.0 (Accelrys, San Diego).

Kovarik Z., Hrvat N.M., Katalinić M., Sit R.K., Paradyse A., Žunec S., Musilek K., Fokin V.V., Taylor P, & Radić Z. (2015). Catalytic soman scavenging by Y337A/F338A acetylcholinesterase mutant assisted with novel site-directed aldoximes. Chemical research in toxicology, 28(5), 1036-1044.

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Homology Modeling of SAPK9 Protein

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The homology model of SAPK9 was made using the MODELLER 9.15 (https://salilab.org/modeller/download_installation.html). The solved crystal structure of the OST1/SnRK2.6 protein from Arabidopsis (PDB ID: 3UC4) was taken as a template for constructing the in silico model of SAPK9. The resulting model was energy minimized using Insight II (2000.1, Accelrys Inc.) followed by stereo-chemical evaluation using MolProbity (http://molprobity.biochem.duke.edu/). The pictorial representations were prepared in PyMol (http://www.pymol.org).

Dey A., Samanta M.K., Gayen S, & Maiti M.K. (2016). The sucrose non-fermenting 1-related kinase 2 gene SAPK9 improves drought tolerance and grain yield in rice by modulating cellular osmotic potential, stomatal closure and stress-responsive gene expression. BMC Plant Biology, 16, 158.

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Modeling Inactive DmpR Dimer Structure

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The inactive DmpR dimer was modelled using the A. aeolicus NtrC1 in complex with ADP (PDB ID, 1ny5) as the template. The dimeric NtrC1 structure was truncated so that only the ATPase domain was retained. The docking of ADP to the DmpR^ΔD structure with loop modelling was performed using the SwissDock server. The initial models were subjected to energy minimization followed by 1 ps of molecular dynamics at 300 K after equilibration. They were finally minimized to a maximum derivative with 1.0 kcal per step using the Discover module in the Insight II program (Accelrys) with the AMBER force field.

Park K.H., Kim S., Lee S.J., Cho J.E., Patil V.V., Dumbrepatil A.B., Song H.N., Ahn W.C., Joo C., Lee S.G., Shingler V, & Woo E.J. (2020). Tetrameric architecture of an active phenol-bound form of the AAA+ transcriptional regulator DmpR. Nature Communications, 11, 2728.

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NMR Structural Modeling of DB[a,l]P-DNA Adduct

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The initial model was based on the NMR
solution structure of the stereochemically analogous 10S-B[a]P-dG adduct^{29 (link)} positioned
in the minor groove in the identical sequence context, replacing the
B[a]P moiety with the DB[a,l]P residue as described above for the deletion duplex.
This model was adopted because the NMR data suggest that the DB[a,l]P residue in the 14S-DB[a,l]P-dG full duplex is positioned
in the minor groove (see Results). Minor close
contacts were alleviated by molecular modeling. Visualization and
model building were performed with INSIGHT II (Accelrys Software,
Inc.). PyMOL (Schrödinger, LLC) was employed to make molecular
images and movies.

Rodríguez F.A., Liu Z., Lin C.H., Ding S., Cai Y., Kolbanovskiy A., Kolbanovskiy M., Amin S., Broyde S, & Geacintov N.E. (2014). Nuclear Magnetic Resonance Studies of an N2-Guanine Adduct Derived from the Tumorigen Dibenzo[a,l]pyrene in DNA: Impact of Adduct Stereochemistry, Size, and Local DNA Sequence on Solution Conformations. Biochemistry, 53(11), 1827-1841.

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EGFR Mutation Analysis by Flow Cytometry

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NIH3T3 cells were obtained from ATCC (CRL-1658) in 2016 and were passaged for less than 6 months after receipt. Full-length human EGFR cDNA (Addgene 23935) was mutagenized using the Stratagene Site-Directed Mutagenesis Kit to produce V441D and V441G mutations. EGFR-containing pLenti-puro (Addgene 17452) was used to produce virus to infect NIH3T3 cells. Cells were infected with empty pLenti plasmid, wild type EGFR, EGFR V441D and EGFR V441G, and analyzed by flow cytometry for antibody binding as performed by others (17 (link)). Cells were analyzed by Western blot to demonstrate equal levels of EGFR expression. 1×10⁶ cells of each type were resuspended in 100uL of 1% BSA in PBS, and incubated with 1ug of either cetuximab or panitumumab for 1 hour at 4°C. Cells were washed with 1% BSA in PBS, and incubated with 1ug of anti-human PE-conjugated secondary antibody (ThermoFisher H10104). Cells were washed and subsequently read on an LSRII flow cytometer. The antibody binding experiment was performed in triplicate. Molecular modeling was conducted using the program Insight II (Accelrys, San Diego).

Strickler J.H., Loree J.M., Ahronian L.G., Parikh A.R., Niedzwiecki D., Pereira A.A., Mckinney M., Korn W.M., Atreya C.E., Banks K.C., Nagy R.J., Meric-Bernstam F., Lanman R.B., Talasaz A., Tsigelny I.F., Corcoran R.B, & Kopetz S. (2017). Genomic landscape of cell-free DNA in patients with colorectal cancer. Cancer discovery, 8(2), 164-173.

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MCT4 Homology Modeling and Validation

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The homology model of MCT4 was created using a sequence alignment (Clustal Omega) [41 (link)] to MCT1 and building the model using the MCT1 homology model previously created [35 (link)] as a template. The large intracellular loop between helices 6 and 7 was removed during development of the model, as it is not thought to contribute to either inhibitor binding or substrate transport [25 (link)]. Insight II (Accelrys Inc.) was used for visualization and Discover 2.98 (Accelrys) was used to minimize the energy of the resulting structures. The intracellular loop and C-terminal tail were added to the MCT1 homology models before simulation. The loop was created with a random conformation using the loop-building function of Insight II as these regions are not predicted to adopt a particular structure due to the high variation in their sequence and length between isoforms. In addition, we have shown previously that the C-terminal tail of MCT1 is not involved in AR-C155858 inhibition [25 (link)]. Coordinates for all the model structures generated in the present study are available as PDB files in Supplementary data.

Nancolas B., Sessions R.B, & Halestrap A.P. (2015). Identification of key binding site residues of MCT1 for AR-C155858 reveals the molecular basis of its isoform selectivity. Biochemical Journal, 466(Pt 1), 177-188.

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Molecular Docking of CK1ε Inhibitor

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Insight II (Accelrys Inc, San Diego, USA) was used for the docking study and structure analysis using the coordinates of CK1ε in complex with PF4800567 (PDB accession code 4HNI).

Yang H., Lee S., Ji H., Kim J.E., Yoo R., Kim J.H., Suk S., Huh C.S., Park J.H., Heo Y.S., Shin H.S., Kim B.G, & Lee K.W. (2019). Orobol, an Enzyme-Convertible Product of Genistein, exerts Anti-Obesity Effects by Targeting Casein Kinase 1 Epsilon. Scientific Reports, 9, 8942.

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Adenosine Structural Analysis and Electrostatic Mapping

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The geometry for adenosine was obtained from InsightII (Accelrys). The ribose sugar was substituted for a methyl group, and the positions of the N−CH₃ bond on both base pairs and the C−H group at the 7 position of 7DA were optimized at the MP2(full)/6-311G** level of theory using Gaussian 09 (Frisch et al. 2009 ) while the rest of the RNA base atoms were constrained to their InsightII position. The electrostatic potential maps of adenosine and 7DA were generated using the Psi4 computational package (Turney et al. 2012 ). Electrostatic potential values were calculated from the frozen core density fitting MP2 method, 6-311++G** basis sets, and aug-cc-pvtz-ri density fitting basis sets. The cube file was imported into Chemcraft (Chemcraft, Version 1.7 [build 375], Zhurko), and the diagram was created by painting the potential values on the van der Waals spheres.

Richardson K.E, & Znosko B.M. (2016). Nearest-neighbor parameters for 7-deaza-adenosine·uridine base pairs in RNA duplexes. RNA, 22(6), 934-942.

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