Ruben Abagyan

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XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification.

Colin A. Smith, Elizabeth J. Want, Grace O'Maille, Ruben Abagyan, Gary Siuzdak
Analytical chemistry
2006

Metabolite profiling in biomarker discovery, enzyme substrate assignment, drug activity/specificity determination, and basic metabolic research requires new data preprocessing approaches to correlate… (More)

ICM - A New Method for Protein Modeling and Design: Applications to Docking and Strucutre Prediction from the Distorted Native Conformation

Ruben Abagyan, Maxim Totrov, Dmitry Kuznetsov
Journal of Computational Chemistry
1994

An efficient methodology, further referred to as ICM, for versatile modeling operations and global energy optimization on arbitrarily fixed multimolecular systems is described. It is aimed at protein… (More)

Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists.

Beili Wu, Ellen Yu-Lin Chien, +12 authors Raymond C. Stevens
Science
2010

Chemokine receptors are critical regulators of cell migration in the context of immune surveillance, inflammation, and development. The G protein-coupled chemokine receptor CXCR4 is specifically… (More)

METLIN: a metabolite mass spectral database.

Colin A. Smith, Grace O'Maille, +6 authors Gary Siuzdak
Therapeutic drug monitoring
2005

Endogenous metabolites have gained increasing interest over the past 5 years largely for their implications in diagnostic and pharmaceutical biomarker discovery. METLIN (http://metlin.scripps.edu), a… (More)

Conserved binding mode of human beta2 adrenergic receptor inverse agonists and antagonist revealed by X-ray crystallography.

Daniel Wacker, Gustavo Fenalti, +4 authors Raymond C. Stevens
Journal of the American Chemical Society
2010

G protein-coupled receptors (GPCRs) represent a large fraction of current pharmaceutical targets, and of the GPCRs, the beta(2) adrenergic receptor (beta(2)AR) is one of the most extensively studied.… (More)

Novel Anchorage of GluR2/3 to the Postsynaptic Density by the AMPA Receptor–Binding Protein ABP

Sapna Srivastava, Pavel Osten, +9 authors Edward B Ziff
Neuron
1998

We report the cloning of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptor-binding protein (ABP), a postsynaptic density (PSD) protein related to glutamate… (More)

Sirtuin 2 inhibitors rescue alpha-synuclein-mediated toxicity in models of Parkinson's disease.

Tiago F Outeiro, Eirene Kontopoulos, +12 authors Aleksey G. Kazantsev
Science
2007

The sirtuins are members of the histone deacetylase family of proteins that participate in a variety of cellular functions and play a role in aging. We identified a potent inhibitor of sirtuin 2… (More)

Virtual ligand screening of the p300/CBP histone acetyltransferase: identification of a selective small molecule inhibitor.

Erin M. Bowers, Gai Yan, +16 authors Philip A Cole
Chemistry & biology
2010

The histone acetyltransferase (HAT) p300/CBP is a transcriptional coactivator implicated in many gene regulatory pathways and protein acetylation events. Although p300 inhibitors have been reported,… (More)

Flexible protein-ligand docking by global energy optimization in internal coordinates.

Eight protein-ligand complexes were simulated by using global optimization of a complex energy function, including solvation, surface tension, and side-chain entropy in the internal coordinate space… (More)

Structure of the human histamine H1 receptor complex with doxepin

Tatsuro Shimamura, Mitsunori Shiroishi, +10 authors So Iwata
Nature
2011

The biogenic amine histamine is an important pharmacological mediator involved in pathophysiological processes such as allergies and inflammations. Histamine H1 receptor (H1R) antagonists are very… (More)

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