Search Results - "Abagyan, Ruben A."

Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases by Cavasotto, Claudio N., Abagyan, Ruben A.

“…The main complicating factor in structure-based drug design is receptor rearrangement upon ligand binding (induced fit). It is the induced fit that complicates…”
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Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling by Arnautova, Yelena A., Abagyan, Ruben A., Totrov, Maxim

“…We report the development of internal coordinate mechanics force field (ICMFF), new force field parameterized using a combination of experimental data for…”
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Discovery of Novel Chemotypes to a G-Protein-Coupled Receptor through Ligand-Steered Homology Modeling and Structure-Based Virtual Screening by Cavasotto, Claudio N, Orry, Andrew J. W, Murgolo, Nicholas J, Czarniecki, Michael F, Kocsi, Sue Ann, Hawes, Brian E, O’Neill, Kim A, Hine, Heather, Burton, Marybeth S, Voigt, Johannes H, Abagyan, Ruben A, Bayne, Marvin L, Monsma, Frederick J

“…Melanin-concentrating hormone receptor 1 (MCH-R1) is a G-protein-coupled receptor (GPCR) and a target for the development of therapeutics for obesity. The…”
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Efficient Synthetic Inhibitors of Anthrax Lethal Factor by Forino, Martino, Johnson, Sherida, Wong, Thiang Y., Rozanov, Dmitri V., Savinov, Alexei Y., Li, Wei, Fattorusso, Roberto, Becattini, Barbara, Orry, Andrew J., Jung, Dawoon, Abagyan, Ruben A., Smith, Jeffrey W., Alibek, Ken, Liddington, Robert C., Strongin, Alex Y., Pellecchia, Maurizio, Vogt, Peter K.

“…Inhalation anthrax is a deadly disease for which there is currently no effective treatment. Bacillus anthracis lethal factor (LF) metalloproteinase is an…”
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Structure-based identification of binding sites, native ligands and potential inhibitors for G-protein coupled receptors by Cavasotto, Claudio N., Orry, Andrew J.W., Abagyan, Ruben A.

“…G‐protein coupled receptors (GPCRs) are the largest family of cell‐surface receptors involved in signal transmission. Drugs associated with GPCRs represent…”
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Representing Receptor Flexibility in Ligand Docking through Relevant Normal Modes by Cavasotto, Claudio N, Kovacs, Julio A, Abagyan, Ruben A

“…Inspired by the current representation of the ligand−receptor binding process, a normal-mode-based methodology is presented to incorporate receptor flexibility…”
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The 1.8 A crystal structure of the dimeric peroxisomal 3-ketoacyl-CoA thiolase of Saccharomyces cerevisiae: implications for substrate binding and reaction mechanism by Mathieu, M, Modis, Y, Zeelen, J P, Engel, C K, Abagyan, R A, Ahlberg, A, Rasmussen, B, Lamzin, V S, Kunau, W H, Wierenga, R K

“…The dimeric, peroxisomal 3-ketoacyl-CoA thiolase catalyses the conversion of 3-ketoacyl-CoA into acyl-CoA, which is shorter by two carbon atoms. This reaction…”
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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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In silico identification of novel EGFR inhibitors with antiproliferative activity against cancer cells by Cavasotto, Claudio N., Ortiz, María A., Abagyan, Ruben A., Piedrafita, F. Javier

“…Inhibition of the epidermal growth factor receptor (EGFR) tyrosine kinase activity by small molecules has proved effective for the treatment of cancer. To the…”
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Ab InitioFolding of Peptides by the Optimal-Bias Monte Carlo Minimization Procedure by Abagyan, Ruben A, Totrov, Maxim

“…Prediction of three-dimensional structures of proteins and peptides by global optimization of the free energy estimate has been attempted without much success…”
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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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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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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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Contact area difference (CAD): a robust measure to evaluate accuracy of protein models by Abagyan, Ruben A., Totrov, Maxim M.

“…A simple unified measure to evaluate the accuracy of three-dimensional atomic protein models is proposed. This measure is a normalized sum of absolute…”
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TNF-alpha convertase enzyme from human arthritis-affected cartilage: isolation of cDNA by differential display, expression of the active enzyme, and regulation of TNF-alpha by Patel, I R, Attur, M G, Patel, R N, Stuchin, S A, Abagyan, R A, Abramson, S B, Amin, A R

“…A snake venom-like protease isolated by a differential display screen between normal and osteoarthritis (OA)-affected cartilage (designated as cSVP) has a cDNA…”
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Modeling, mutagenesis, and structural studies on the fully conserved phosphate-binding loop (Loop 8) of triosephosphate isomerase: Toward a new substrate specificity by Norledge, Brian V., Lambeir, Anne M., Abagyan, Ruben A., Rottmann, Antje, Fernandez, Anna M., Filimonov, Vladimir V., Peter, Martin G., Wierenga, Rik K.

“…Loop 8 (residues 232–242) in triosephosphate isomerase (TIM) is a highly conserved loop that forms a tight binding pocket for the phosphate moiety of the…”
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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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New methodology for computer-aided modelling of biomolecular structure and dynamics. 1. Non-cyclic structures by Mazur, A K, Abagyan, R A

“…A general methodology is proposed for the conformational modelling of biomolecular systems. The approach allows one: (i) to describe the system under…”
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New methodology for computer-aided modelling of biomolecular structure and dynamics. 2. Local deformations and cycles by Abagyan, R A, Mazur, A K

“…A new methodology for the conformational modelling of biomolecular systems (1) is extended to local deformations of chain molecules and to flexible molecular…”
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Proposed structure for the DNA-binding domain of the helix-loop-helix family of eukaryotic gene regulatory proteins by Gibson, T J, Thompson, J D, Abagyan, R A

“…A modelled tertiary structure for the dimeric HLH domain of the E47 protein is presented. Structural information was obtained from the aligned sequences of >…”
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