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XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification.
- Colin A. Smith, E. Want, Grace O'Maille, R. Abagyan, G. Siuzdak
- BiologyAnalytical chemistry
- 7 January 2006
An LC/MS-based data analysis approach, XCMS, which incorporates novel nonlinear retention time alignment, matched filtration, peak detection, and peak matching, and is demonstrated using data sets from a previously reported enzyme knockout study and a large-scale study of plasma samples.
Structures of the CXCR4 Chemokine GPCR with Small-Molecule and Cyclic Peptide Antagonists
Five independent crystal structures of CXCR4 bound to an antagonist small molecule IT1t and a cyclic peptide CVX15 at 2.5 to 3.2 angstrom resolution reveal a consistent homodimer with an interface including helices V and VI that may be involved in regulating signaling.
ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
It is concluded that the most promising detailed approach to the protein‐folding problem would consist of some coarse global sampling strategy combined with the local energy minimization in the torsion coordinate space.
METLIN: A Metabolite Mass Spectral Database
- Colin A. Smith, Grace O' Maille, G. Siuzdak
- Chemistry, BiologyTherapeutic drug monitoring
- 1 December 2005
METLIN includes an annotated list of known metabolite structural information that is easily cross-correlated with its catalogue of high-resolution Fourier transform mass spectrometry (FTMS) spectra, tandem mass spectrumetry (MS/MS) Spectra, and LC/MS data.
Virtual ligand screening of the p300/CBP histone acetyltransferase: identification of a selective small molecule inhibitor.
Structure of the human histamine H1 receptor complex with doxepin
Light is shed on the molecular basis of H1R antagonist specificity against H1r, demonstrating how minor differences in receptors lead to pronounced selectivity differences with small molecules.
Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins.
An efficient way to make a random step in a Monte Carlo procedure given knowledge of the energy or statistical properties of conformational subspaces is found, and the BPMC procedure is applied to the structure prediction of 12- and 16-residue synthetic peptides and the determination of protein structure from NMR data.
Sirtuin 2 inhibitors rescue alpha-synuclein-mediated toxicity in models of Parkinson's disease.
A potent inhibitor of sirtuin 2 (SIRT2) was identified and inhibition of SIRT2 rescued alpha-synuclein toxicity and modified inclusion morphology in a cellular model of Parkinson's disease, suggesting a link between neurodegeneration and aging.
Novel Anchorage of GluR2/3 to the Postsynaptic Density by the AMPA Receptor–Binding Protein ABP
Pocketome via Comprehensive Identification and Classification of Ligand Binding Envelopes*
A new computational algorithm for the accurate identification of ligand binding envelopes rather than surface binding sites is developed and the data base of the known and predicted binding pockets for the human proteome structures, the human pocketome, was collected and classified.