Docking validation of Dud778-dUTPase cocrystal structure.

Slides:

Advertisements

Similar presentations

L. Brillet (CEA) – ANR meeting – META08 Hammamet 1/18 validation ANR meeting - 28/10/2008 CEA Grenoble - DSV/iRTSV/CMBA.

Advertisements

Knowing When to Give Up Sensible Evaluation in Virtual Screening for Drug Discovery Gwyn Skone Stephen Cameron and Irina Voiculescu.

Summary Molecular surfaces QM properties presented on surface Compound screening Pattern matching on surfaces Martin Swain Critical features Dave Whitley.

BL5203: Molecular Recognition & Interaction Lecture 5: Drug Design Methods Ligand-Protein Docking (Part I) Prof. Chen Yu Zong Tel:

In silico discovery of inhibitors using structure-based approaches Jasmita Gill Structural and Computational Biology Group, ICGEB, New Delhi Nov 2005.

Bioinformatics MEDC601 Lecture by Brad Windle Ph# Office: Massey Cancer Center, Goodwin Labs Room 319 Web site for lecture:

Development of computational tools for

CYB561 homology modeling. CYB561 homology modeling.A, Close-up of mutation G88R in CYB561. The protein is shown in ribbon presentation in gray, the heme.

Molecular Docking Profacgen. The interactions between proteins and other molecules play important roles in various biological processes, including gene.

Volume 19, Issue 8, Pages (August 2011)

Virtual Screening.

A, structure drawing of LY

AG-221 structure and binding characteristics.

Volume 12, Issue 1, Pages (March 2004)

Protein microarrays for validation of antibodies.

Interaction networks of the regulated phosphoproteins.

Ligand Binding to the Voltage-Gated Kv1

Volume 19, Issue 8, Pages (August 2011)

Combined regulatory network with three identified modules.

David Rodríguez, José Brea, María Isabel Loza, Jens Carlsson Structure

A, IC50 dose–response curves of SYD985, T-DM1, and ADC isotype control in all USC cell lines tested in vitro (i.e., HER2 3+ cell lines, P =

Stereoimage of three independent docking simulations of the interaction between clopidogrel acyl 1-β-d-glucuronide and the active site of CYP2C8. Stereoimage.

Volume 84, Issue 4, Pages (April 2003)

Changes in tumor sizes, CA-125, serum ceruloplasmin, and copper levels in 5 patients with platinum-resistant high-grade epithelial ovarian cancer who received.

GA blocks HIF activity and reduces HIF target expression.

A, IGFBP-3 knockdown via siRNA using real-time qRT-PCR analysis.

Diagnostic plots of the TGI PKPD model fitted to the A677 TGI data.

Expression analysis of IGFBP-3 using human whole-genome microarray.

Skin tumor size following ligand activation of PPARβ/δ and inhibition of COX2. Skin tumor size following ligand activation of PPARβ/δ and inhibition of.

Induction of CDKN1A (□), MDM2 (◊), and GADD45A (○) in ML-1 cells by 50 cGy X-rays delivered at 0.28 cGy/min. Induction of CDKN1A (□), MDM2 (◊), and GADD45A.

Variation in dUTPase expression in cell lines.

A, cytotoxicity induced on HER2 3+ USC (ARK-2), HER2 0/1+ USC (ARK-4), and ARK-2/ARK-4 cocultures with 1 μg/mL of SYD985, T-DM1, and ADC isotype control.

Illustration of a stably tethered structure made by the DNL method.

Perifosine affects membrane distribution of HA-Akt1 and Akt1-PH domain constructs. Perifosine affects membrane distribution of HA-Akt1 and Akt1-PH domain.

Interaction of MAPJD with E-box sequence of the RIOK1 gene.

Simulations to guide drug design strategies for anti–Bcl-2 therapy.

Reduced BAI1 expression is associated with breast cancer patient survival. Reduced BAI1 expression is associated with breast cancer patient survival. A,

Analysis of thermal stability and aggregation properties before and after disulfide stabilization of the pMHCI complex. Analysis of thermal stability and.

CAT displays very high in vivo stability as exemplified by a rat PK study. CAT displays very high in vivo stability as exemplified by a rat.

Comparison of the predicted binding models of mHA1, mHA6, and mHA 11 to the tubulin protein with that of DAMA-colchicine in the crystal structure. Comparison.

Proposed model for the role of PALB2 in linking BRCA1 with BRCA2 and RAD51 in a pathway of HR. We propose that BRCA1 binds to the NH2 terminus of PALB2.

Induction of cell death in prostate cancer cells by SAHA and ZOL

Cisplatin plus PTUPB decreases proliferation and angiogenesis but increases apoptosis as determined by immunohistochemical (IHC) analysis. Cisplatin plus.

DNA damage-induced RPA foci in asynchronous cells labeled with BUdR.

A, protein structure and functional domains of hdbpB/YB-1, hdbpA, hdbpC, NF-YA, NF-YB, and NF-YC. A, protein structure and functional domains of hdbpB/YB-1,

Structural model of Y764_V765insHH.

Immunohistochemical detection of nuclear and cytoplasmic YB-1 in osteosarcoma and synovial sarcoma. Immunohistochemical detection of nuclear and cytoplasmic.

Angiogenesis in tumors formed by cells varying in the expression of CXCR2. Angiogenesis in tumors formed by cells varying in the expression of CXCR2. A,

GA reduces the growth of Caki-1 tumor xenografts.

Modeling of EGFR exon 20 insertions using the 3-dimensional structure of the EGFR kinase domain predicts different interactions with the erlotinib-binding.

Positions of the EGFR exon 20 insertions identified over a 3-year period and comparison with the spectrum of EGFR exon 19 and HER2 insertion mutations.

LY induces replication stress and depletes the pool of available RPA2 for binding to DNA. HeLa cells were treated with 0.4% DMSO, 100 nmol/L LY

Colony formation of K-562 cells after 24 h (upper panel) or 48 h (lower panel) exposure to ErPC3 (20 μm) and ASO-bcr (10 μm), respectively. Colony formation.

Immunohistochemical analysis of dUTPase in human breast adenocarcinoma

Tumor and serum levels of murine IL-12.

Binding and antiproliferative effects of ANG4043 and anti-HER2 mAbs on tumor cells. Binding and antiproliferative effects of ANG4043 and anti-HER2 mAbs.

Xenograft regrowth studies.

Molecular docking of celastrol with Hsp90 and Hsp90-Cdc37 complex.

A, P causes G2-M arrest with apoptosis in asynchronous population of PC-3 when exposed to 1.5 and 5 μmol/L P for various time points. A, P

Ki-67 expression in M31- and H3-treated tumors (A) and respective Ki-67 labeling indices in the two groups of tumors (B). Ki-67 expression in M31- and.

A, tumor growth studies in H1975 tumor–bearing mice.

Thermodynamic cycle for ligand binding to a periplasmic-BP.

Influence of ASGR2 expression on survival.

Structure of the HLA-DR10 β subunit and ligand binding sites.

Analysis of CF31 RXR-α binding.

Predicted pathogenic BRCA1 amino acid substitutions are confined to the evolutionarily conserved N- and C-terminal domains. Predicted pathogenic BRCA1.

Rapid nucleotide exchange allows irreversible interactions between GDP-bound KRASG12C (middle) and ARS-853 (right). Rapid nucleotide exchange allows irreversible.

E2F4 program is predictive of the efficacy of intravesical BCG immunotherapy in NMIBC. A, the survival curves of intravesical therapy-treated and untreated.

Fig. 4 The oxidized and reduced forms of the A2 domain have different dynamics and stresses. The oxidized and reduced forms of the A2 domain have different.

Model of the change in receptor structure on engagement of the ligand IFN-γ. Model of the change in receptor structure on engagement of the ligand IFN-γ.

Presentation transcript:

Docking validation of Dud778-dUTPase cocrystal structure. Docking validation of Dud778-dUTPase cocrystal structure. A, Dud778 as observed in the X-ray structure (1Q5H; green). The atom-type colored conformation of Dud778 is predicted by Genetic Optimization for Ligand Docking. B, superimposition of a representative compound, colored by atom type, with X-ray determined Dud778 conformation (green). The compound was selected from database screening that favorably interacts with the ligand binding domain by efficiently filling the deep cavity. Peter M. Wilson et al. Mol Cancer Ther 2008;7:3029-3037 ©2008 by American Association for Cancer Research