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Accelrys 3d structural models
3d Structural Models, supplied by Accelrys, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Article Title: Machine Learning-Guided Discovery of AcrB and MexB Efflux Pump Inhibitors.
Article Snippet: [5] This QSAR-based system, developed by Accelrys Inc., makes predictions of a range of toxicological endpoints.

Article Title: TSCC: Two-Stage Combinatorial Clustering for virtual screening using protein-ligand interactions and physicochemical features
Article Snippet: We employed our docking tool, GEMDOCK, to generate protein-ligand interactions and used the Accelrys Cerius QSAR module for obtaining physicochemical features of complexes.

Article Title: Fragment-based structural exploration and chemico-biological interaction study of HDAC3 inhibitors through non-linear pattern recognition, chemical space, and binding mode of interaction analysis.
Article Snippet: HDAC3 is an emerging target for the identification and discovery of novel drug candidates against several disease conditions including cancer.. Here, a fragment-based non-linear machine learning (ML) method along with chemical space exploration followed by a structure-based binding mode of interaction analysis study was carried out on some HDAC3 inhibitors to obtain the key structural features modulating HDAC3 inhibition.. Both the ML and chemical space analysis identified several physicochemical and structural properties namely lipophilicity, polar and relative polar surface area, arylcarboxamide moiety, bulky fused aromatic group, n-alkyl, and cinnamoyl moieties, the higher number of oxygen atoms, p-electrons for the substituted tetrahydrofuronaphthodioxolone moiety favorable for higher HDAC3 inhibition.

Article Title: Applications of Model-Based Target Pharmacology Assessment in Defining Drug Design and DMPK Strategies: GSK Experiences.
Article Snippet: Many critical decisions faced in early discovery require a thorough understanding of the dynamic behavior of pharmacological pathways following target engagement.. From fundamental decisions on the optimal target to pursue and the ultimate drug product profile (combination of modality, potency, and compound properties) expected to elicit the desired clinical outcome to tactical program decisions such as what chemical series to pursue, what chemical properties require optimization, and what compounds to synthesize and progress, all demand detailed consideration of pharmacodynamics.. Model-based target pharmacology assessment (mTPA) is a computational approach centered around large-scale virtual exploration of pharmacokinetic and pharmacodynamic models built early in discovery to guide these decisions.

Article Title: A Mini‐Review on the Application of Computational Strategies in Multi‐Armed Star‐PEG Polymeric Micelles for Drug Delivery
Article Snippet: Syarah Mat Udin,[a] Hasmerya Maarof,*[a] and Norizah Abdul Rahman[b] Wiley VCH Dienstag, 14.11.2023 2343 / 327584 [S. 209/222] 1 ChemistrySelect 2023, 8, e202301022 (1 of 14) © 2023 Wiley-VCH GmbH ChemistrySelect www.chemistryselect.org Review doi.org/10.1002/slct.202301022 Polymeric micelles (PM) are amphiphilic block copolymers that can form nanoscopic core/shell structures, making them highly effective for drug delivery systems (DDS).. Multi-armed starshaped poly(ethylene glycol) (PEG) polymers, a promising type of PM, provide a regulated release of drugs and can be integrated with numerous endpoints to create multifunctional drug delivery systems capable of transporting a large number of drugs.. Star-PEG polymers can also be cross-linked to create three dimensional hydrogels with variable functionalities and sizes, increasing blood flow and reducing unanticipated drug release.

Article Title: In silico exploration of graphene nanoflakes: From DFT simulations to machine learning-driven toxicity predictions.
Article Snippet: The present theoretical work provides a ground-breaking and comprehensive study of graphene nanoflakes integrating Density Functional Theory (DFT) simulations, toxicity predictions and a machine learning approach.. The properties of graphene nanoflakes as a function of size, shape, and symmetry are systematically analysed using DFT calculations.. The interaction of these nanoflakes with human proteins and cell membranes, considered as Molecular Initiating Events for diverse Adverse Outcome Pathways, is explored to infer potential toxicity effects.

Article Title: Senna makki and other active phytochemicals: Myths and realities behind covid19 therapeutic interventions
Article Snippet: The protocol to generate a 3D-QSAR pharmacophore model for the given training set and validation with a test set takes place simultaneously in BIOVIA DS resulting in a detailed report with 10 hypothesis models generated with different statistical parameters.

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Article Title: Epigenetic Inhibition of HDAC7 by Daidzein isolated from Macrotyloma uniflorum: A potential therapeutic approach in leukemia in silico, in-vitro and in-vivo.
Article Snippet: 1 Department of Biotechnology at Jamia Hamdard, Delhi 110062, India 2 Department of Phrmacognosy & Phytochemistry at Jamia Hamdard, Delhi 110062, India 3 Department of Obstetrics and Gynecology at Jamia Hamdard, Delhi 110062, India Abstract Leukaemia remains a critical haematologic malignancy, where current therapies offer limited efficacy and are frequently associated with significant toxicity.. Epigenetic dysregulation, particularly aberrant histone deacetylase (HDAC) activity, promotes uncontrolled proliferation and suppression of apoptosis in leukaemic cells, with HDAC7 identified as a central driver of disease progression.. Daidzein, a natural isoflavonoid from Macrotyloma uniflorum, represents a promising plantderived HDAC inhibitor.

Positive Control:

Article Title: Epigenetic Inhibition of HDAC7 by Daidzein isolated from Macrotyloma uniflorum: A potential therapeutic approach in leukemia in silico, in-vitro and in-vivo.
Article Snippet: 1 Department of Biotechnology at Jamia Hamdard, Delhi 110062, India 2 Department of Phrmacognosy & Phytochemistry at Jamia Hamdard, Delhi 110062, India 3 Department of Obstetrics and Gynecology at Jamia Hamdard, Delhi 110062, India Abstract Leukaemia remains a critical haematologic malignancy, where current therapies offer limited efficacy and are frequently associated with significant toxicity.. Epigenetic dysregulation, particularly aberrant histone deacetylase (HDAC) activity, promotes uncontrolled proliferation and suppression of apoptosis in leukaemic cells, with HDAC7 identified as a central driver of disease progression.. Daidzein, a natural isoflavonoid from Macrotyloma uniflorum, represents a promising plantderived HDAC inhibitor.



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(a) Graphical result from secondary structure prediction of Hyde C1 using PSIPRED. (b) Helical wheel diagram of Hyde C1 and polar and non-polar amino acids, and their locations in peptide can be observed (c) The Hyde C1 3D structure contains α-helix, as predicted by I-TASSER. The 3D structure model visualized using Accelrys discovery studio visualizer software.

Journal: Scientific Reports

Article Title: Discovery of hyde C1 a broad spectrum antimicrobial peptide derived from chicory

doi: 10.1038/s41598-025-19166-5

Figure Lengend Snippet: (a) Graphical result from secondary structure prediction of Hyde C1 using PSIPRED. (b) Helical wheel diagram of Hyde C1 and polar and non-polar amino acids, and their locations in peptide can be observed (c) The Hyde C1 3D structure contains α-helix, as predicted by I-TASSER. The 3D structure model visualized using Accelrys discovery studio visualizer software.

Article Snippet: The 3D structure model visualized using Accelrys discovery studio visualizer software.

Techniques: Software