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BioSolveIT GmbH flexx program leadit 2.1.8
Flexx Program Leadit 2.1.8, supplied by BioSolveIT GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Article Title: Development of colorimetric HTS assay of cytochrome p450 for ortho-specific hydroxylation, and engineering of CYP102D1 with enhanced catalytic activity and regioselectivity.
Article Snippet: Development of Colorimetric HTS Assay of Cytochrome P450 for orthoSpecific Hydroxylation, and Engineering of CYP102D1 with Enhanced Catalytic Activity and Regioselectivity High-speed activity: A general HTS assay method for ortho-specific hydroxylation by P450 enzymes is presented.. In order to screen for P450 variants with higher hydroxylation activities, an indirect HTS assay method to sense aldehyde molecules generated from O-dealkylation reaction of chemically permethylated substrate was developed.

Article Title: Characterization of a novel family VIII esterase EstM2 from soil metagenome capable of hydrolyzing estrogenic phthalates
Article Snippet: For docking experiments using FlexX program, standard parameters as implemented in the 2.1.3 release of the LeadIT (BioSolveIT, GmbH, Germany) were used for iterative growing and subsequent scoring of the target-bound conformations and orientations (here, called solutions) and the active site was defined as the collection of amino acids enclosed within a 10 Å radius sphere centered on the reference ligand [ ].

Article Title: Characterization of a topologically unique oxygenase from Sphingobium sp. PNB capable of catalyzing a broad spectrum of aromatics.
Article Snippet: Accepted Manuscript Title: Characterization of a topologically unique oxygenase from Sphingobium sp. PNB capable of catalyzing a broad spectrum of aromatics Authors: Pratick Khara, Madhumita Roy, Joydeep Chakraborty, Arindam Dutta, Tapan K. Dutta PII: S0141-0229(17)30193-X DOI: https://doi.org/10.1016/j.enzmictec.2017.10.006 Reference: EMT 9145 To appear in: Enzyme and Microbial Technology Received date: 1-3-2017 Revised date: 25-8-2017 Accepted date: 16-10-2017 Please cite this article as: Khara Pratick, Roy Madhumita, Chakraborty Joydeep, Dutta Arindam, Dutta Tapan K.Characterization of a topologically unique oxygenase from Sphingobium sp.PNB capable of catalyzing a broad spectrum of aromatics.Enzyme and Microbial Technology https://doi.org/10.1016/j.enzmictec.2017.10.006 This is a PDF file of an unedited manuscript that has been accepted for publication.. As a service to our customers we are providing this early version of the manuscript.. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form.

Article Title: Design of Curcumin and Flavonoid Derivatives with Acetylcholinesterase and Beta-Secretase Inhibitory Activities Using in Silico Approaches
Article Snippet: Docking process was done using FlexX program in BioSolveIT LeadIt 2.0.2 [ ].

Article Title: Synthesis, cyclooxygenase inhibitory effects, and molecular modeling study of 4-aryl-5-(4-(methylsulfonyl)phenyl)-2-alkylthio and -2-alkylsulfonyl-1H-imidazole derivatives.
Article Snippet: a Department of Medicinal Chemistry, Faculty of Pharmacy and Drug Design & Development Research Center, Tehran University of Medical Sciences, Tehran 14176, Iran b Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, 2142-L Katz Group Centre for Pharmacy and Health Research, Edmonton, Alberta, Canada T6G 2E9 c Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Hacettepe, Sihhiye, 06100 Ankara, Turkey d Department of Toxicology and Pharmacology, Faculty of Pharmacy and Rational Drug Use Research Center, Tehran University of Medical Sciences, Tehran, Iran e Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran 14176, Iran

Article Title: Rehabilitating drug-induced long-QT promoters: In-silico design of hERG-neutral cisapride analogues with retained pharmacological activity
Article Snippet: FlexX: The FlexX program (v.4.0) from BioSolveIT was also used.

Protein Binding:

Article Title: Establishment of correlation between in-silico and in-vitro test analysis against Leishmania HGPRT to inhibitors.
Article Snippet: Hypoxanthine Phosphoribosyltransferase (HGPRT; EC 2.4.2.8) is a central enzyme in the purine recycling pathway of all protozoan parasites.. Protozoan parasites cannot synthesize purine bases (DNA/RNA) which is essential for survival as lack of de-novo pathway.. Thus its good target for drug design and discovery as inhibition leads to cessation of replication.

Binding Assay:

Article Title: Search for human DNA topoisomerase II poisons in the group of 2,5-disubstituted-1,3,4-thiadiazoles.
Article Snippet: .. Docking studies were conducted by means of the FlexX program20 as implemented in LeadIT package (BioSolveIT, Sankt Augustin, Germany)21 using a model of human DNA topoII binding site complexed with etoposide (PDB id: 3QX322) as a native ligand. ..



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BioSolveIT GmbH flexx program leadit 2.1.8
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The graph is divided into two phases, depicted on the left and the right, respectively. On the left half of the chart, we describe the selection of the best receptor and docking protocol combination; snapshots from MD simulations of ~ 800 ns were clustered and centroids were examined for their ROC performance (ability to discriminate between decoys and known hits). The best performing pair was “2JFZclstr3” as the receptor (derived from the PDB structure 2JFZ, as described in the Methods section) and docking was performed with <t>FlexX</t> <t>(BiosolveIT),</t> as described in the Methods section. The flowchart on the right-hand side is the actual virtual screening protocol that employs the validated 2JFZclstr3-FlexX (receptor and docking protocol) pair, including the experimental biophysical hit validation using SPR. The screening library employed was AnalytiCon’s MEGx natural products library.
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The graph is divided into two phases, depicted on the left and the right, respectively. On the left half of the chart, we describe the selection of the best receptor and docking protocol combination; snapshots from MD simulations of ~ 800 ns were clustered and centroids were examined for their ROC performance (ability to discriminate between decoys and known hits). The best performing pair was “2JFZclstr3” as the receptor (derived from the PDB structure 2JFZ, as described in the Methods section) and docking was performed with <t>FlexX</t> <t>(BiosolveIT),</t> as described in the Methods section. The flowchart on the right-hand side is the actual virtual screening protocol that employs the validated 2JFZclstr3-FlexX (receptor and docking protocol) pair, including the experimental biophysical hit validation using SPR. The screening library employed was AnalytiCon’s MEGx natural products library.
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BioSolveIT GmbH flexx program biosolveit leadit
The graph is divided into two phases, depicted on the left and the right, respectively. On the left half of the chart, we describe the selection of the best receptor and docking protocol combination; snapshots from MD simulations of ~ 800 ns were clustered and centroids were examined for their ROC performance (ability to discriminate between decoys and known hits). The best performing pair was “2JFZclstr3” as the receptor (derived from the PDB structure 2JFZ, as described in the Methods section) and docking was performed with <t>FlexX</t> <t>(BiosolveIT),</t> as described in the Methods section. The flowchart on the right-hand side is the actual virtual screening protocol that employs the validated 2JFZclstr3-FlexX (receptor and docking protocol) pair, including the experimental biophysical hit validation using SPR. The screening library employed was AnalytiCon’s MEGx natural products library.
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The graph is divided into two phases, depicted on the left and the right, respectively. On the left half of the chart, we describe the selection of the best receptor and docking protocol combination; snapshots from MD simulations of ~ 800 ns were clustered and centroids were examined for their ROC performance (ability to discriminate between decoys and known hits). The best performing pair was “2JFZclstr3” as the receptor (derived from the PDB structure 2JFZ, as described in the Methods section) and docking was performed with <t>FlexX</t> <t>(BiosolveIT),</t> as described in the Methods section. The flowchart on the right-hand side is the actual virtual screening protocol that employs the validated 2JFZclstr3-FlexX (receptor and docking protocol) pair, including the experimental biophysical hit validation using SPR. The screening library employed was AnalytiCon’s MEGx natural products library.
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BioSolveIT GmbH flexx program biosolveit leadit 2.0.2
The graph is divided into two phases, depicted on the left and the right, respectively. On the left half of the chart, we describe the selection of the best receptor and docking protocol combination; snapshots from MD simulations of ~ 800 ns were clustered and centroids were examined for their ROC performance (ability to discriminate between decoys and known hits). The best performing pair was “2JFZclstr3” as the receptor (derived from the PDB structure 2JFZ, as described in the Methods section) and docking was performed with <t>FlexX</t> <t>(BiosolveIT),</t> as described in the Methods section. The flowchart on the right-hand side is the actual virtual screening protocol that employs the validated 2JFZclstr3-FlexX (receptor and docking protocol) pair, including the experimental biophysical hit validation using SPR. The screening library employed was AnalytiCon’s MEGx natural products library.
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The graph is divided into two phases, depicted on the left and the right, respectively. On the left half of the chart, we describe the selection of the best receptor and docking protocol combination; snapshots from MD simulations of ~ 800 ns were clustered and centroids were examined for their ROC performance (ability to discriminate between decoys and known hits). The best performing pair was “2JFZclstr3” as the receptor (derived from the PDB structure 2JFZ, as described in the Methods section) and docking was performed with <t>FlexX</t> <t>(BiosolveIT),</t> as described in the Methods section. The flowchart on the right-hand side is the actual virtual screening protocol that employs the validated 2JFZclstr3-FlexX (receptor and docking protocol) pair, including the experimental biophysical hit validation using SPR. The screening library employed was AnalytiCon’s MEGx natural products library.
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The graph is divided into two phases, depicted on the left and the right, respectively. On the left half of the chart, we describe the selection of the best receptor and docking protocol combination; snapshots from MD simulations of ~ 800 ns were clustered and centroids were examined for their ROC performance (ability to discriminate between decoys and known hits). The best performing pair was “2JFZclstr3” as the receptor (derived from the PDB structure 2JFZ, as described in the Methods section) and docking was performed with FlexX (BiosolveIT), as described in the Methods section. The flowchart on the right-hand side is the actual virtual screening protocol that employs the validated 2JFZclstr3-FlexX (receptor and docking protocol) pair, including the experimental biophysical hit validation using SPR. The screening library employed was AnalytiCon’s MEGx natural products library.

Journal: Communications chemistry

Article Title: Decrypting a Cryptic Allosteric Pocket in H. pylori Glutamate Racemase

doi: 10.1038/s42004-021-00605-z

Figure Lengend Snippet: The graph is divided into two phases, depicted on the left and the right, respectively. On the left half of the chart, we describe the selection of the best receptor and docking protocol combination; snapshots from MD simulations of ~ 800 ns were clustered and centroids were examined for their ROC performance (ability to discriminate between decoys and known hits). The best performing pair was “2JFZclstr3” as the receptor (derived from the PDB structure 2JFZ, as described in the Methods section) and docking was performed with FlexX (BiosolveIT), as described in the Methods section. The flowchart on the right-hand side is the actual virtual screening protocol that employs the validated 2JFZclstr3-FlexX (receptor and docking protocol) pair, including the experimental biophysical hit validation using SPR. The screening library employed was AnalytiCon’s MEGx natural products library.

Article Snippet: Two different docking programs where then used since each takes a different approach for ligand placement and for searching minimum energy confirmations: FlexX (part of LeadIT available from BioSolveIT GmbH) 51 – 52 and MOE 2016 38 .

Techniques: Selection, Derivative Assay, Biomarker Discovery