Search Results - "Abagyan, R"

Stabilization of G-Quadruplex DNA with Platinum(II) Schiff Base Complexes: Luminescent Probe and Down-Regulation of c-myc Oncogene Expression by Wu, Peng, Ma, Dik-Lung, Leung, Chung-Hang, Yan, Siu-Cheong, Zhu, Nianyong, Abagyan, R., Che, Chi-Ming

“…The interactions of a series of platinum(II) Schiff base complexes with c‐myc G‐quadruplex DNA were studied. Complex [PtL1a] (1 a;…”
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Identification of Protein–Protein Interaction Sites from Docking Energy Landscapes by Fernández-Recio, Juan, Totrov, Maxim, Abagyan, Ruben

“…Protein recognition is one of the most challenging and intriguing problems in structural biology. Despite all the available structural, sequence and…”
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Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations by Bordner, A. J., Abagyan, R. A.

“…We have developed a method to both predict the geometry and the relative stability of point mutants that may be used for arbitrary mutations. The geometry…”
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ICM-DISCO docking by global energy optimization with fully flexible side-chains by Fernández-Recio, Juan, Totrov, Maxim, Abagyan, Ruben

“…The ICM‐DISCO (Docking and Interface Side‐Chain Optimization) protein–protein‐docking method is a direct stochastic global energy optimization from multiple…”
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Discovery of antiandrogen activity of nonsteroidal scaffolds of marketed drugs by Bisson, W.H, Cheltsov, A.V, Bruey-Sedano, N, Lin, B, Chen, J, Goldberger, N, May, L.T, Christopoulos, A, Dalton, J.T, Sexton, P.M, Zhang, X.-K, Abagyan, R

“…Finding good drug leads de novo from large chemical libraries, real or virtual, is not an easy task. High-throughput screening is often plagued by low hit…”
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Soft protein–protein docking in internal coordinates by Fernández‐Recio, Juan, Totrov, Maxim, Abagyan, Ruben

“…The association of two biological macromolecules is a fundamental biological phenomenon and an unsolved theoretical problem. Docking methods for ab initio…”
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Novel Anchorage of GluR2/3 to the Postsynaptic Density by the AMPA Receptor–Binding Protein ABP by Srivastava, S, Osten, P, Vilim, F.S, Khatri, L, Inman, G, States, B, Daly, C, DeSouza, S, Abagyan, R, Valtschanoff, J.G, Weinberg, R.J, Ziff, E.B

“…We report the cloning of α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptor–binding protein (ABP), a postsynaptic density (PSD) protein…”
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Spatial chemical distance based on atomic property fields by Grigoryan, A. V., Kufareva, I., Totrov, M., Abagyan, R. A.

“…Similarity of compound chemical structures often leads to close pharmacological profiles, including binding to the same protein targets. The opposite, however,…”
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Discovery of a Drug-Like G-Quadruplex Binding Ligand by High-Throughput Docking by Ma, Dik-Lung, Lai, Tat-Shing, Chan, Fung-Yi, Chung, Wai-Hong, Abagyan, R., Leung, Yun-Chung, Wong, Kwok-Yin

“…A new G‐quadruplex binding ligand, namely 1H‐pyrazole‐3‐carboxy‐4‐methyl‐5‐phenyl‐(1H‐indol‐3‐ylmethylene)hydrazide, was identified from a database of 100 000…”
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Accurate Transferable Model for Water, n-Octanol, and n-Hexadecane Solvation Free Energies by Bordner, A. J, Cavasotto, C. N, Abagyan, R. A

“…We present a fast continuum method for the calculation of solvation free energies. It is based on a continuum electrostatics model with MMFF94 atomic charges…”
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Do aligned sequences share the same fold? by Abagyan, Ruben A., Batalov, Serge

“…Sequence comparison remains a powerful tool to assess the structural relatedness of two proteins. To develop a sensitive sequence-based procedure for fold…”
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REVCOM: a robust Bayesian method for evolutionary rate estimation by Bordner, Andrew J., Abagyan, Ruben

“…Motivation: Evolutionary conservation estimated from a multiple sequence alignment is a powerful indicator of the functional significance of a residue and…”
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Direct Derivation of van der Waals Force Field Parameters from Quantum Mechanical Interaction Energies by Bordner, A. J, Cavasotto, C. N, Abagyan, R. A

“…van der Waals force field parameters are difficult to determine from only experimental data because of the insufficient data-to-parameter ratio, particularly…”
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Structure-based development of target-specific compound libraries by Orry, Andrew J.W., Abagyan, Ruben A., Cavasotto, Claudio N.

“…The discovery of new therapeutics can be expedited by the design of structure-based, target specific libraries that can save time and money and can also lead…”
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TSG101 may be the prototype of a class of dominant negative ubiquitin regulators by Koonin, Eugene V, Abagyan, Ruben A

“…The TSG101 gene has been implicated in sporadic breast cancer. Knockout of the murine orthologue resulted in fibroblast transformation and ability to form…”
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Design, Creation, and Characterization of a Stable, Monomeric Triosephosphate Isomerase by Borchert, Torben V., Abagyan, Ruben, Jaenicke, Rainer, Wierenga, Rik K.

“…Protein engineering on trypanosomal triosephosphate isomerase (TIM) converted this oligomeric enzyme into a stable, monomeric protein that is enzymatically…”
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Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR by Filikov, A V, Mohan, V, Vickers, T A, Griffey, R H, Cook, P D, Abagyan, R A, James, T L

“…Binding of the Tat protein to TAR RNA is necessary for viral replication of HIV-1. We screened the Available Chemicals Directory (ACD) to identify ligands to…”
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Adverse Effects of Cholinesterase Inhibitors in Dementia, According to the Pharmacovigilance Databases of the United-States and Canada by Ali, Thibault B, Schleret, Thomas R, Reilly, Brian M, Chen, Winston Yuchen, Abagyan, Ruben

“…This survey analyzes two national pharmacovigilance databases in order to determine the major adverse reactions observed with the use of cholinesterase…”
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XCMS:  Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification by Smith, Colin A, Want, Elizabeth J, O'Maille, Grace, Abagyan, Ruben, Siuzdak, Gary

“…Metabolite profiling in biomarker discovery, enzyme substrate assignment, drug activity/specificity determination, and basic metabolic research requires new…”
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Towards protein folding by global energy optimization by Abagyan, Ruben A.

“…Different components of the theoretical protein folding problem are evaluated critically. It is argued that: (i) as a rule, small- and medium-sized proteins…”
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