Works matching AU Abagyan, Ruben

Results: 130

SimiCon: a web tool for protein–ligand model comparison through calculation of equivalent atomic contacts.

Published in:

Bioinformatics, 2010, v. 26, n. 21, p. 2784, doi. 10.1093/bioinformatics/btq504

By:

Rueda, Manuel;
Katritch, Vsevolod;
Raush, Eugene;
Abagyan, Ruben

Publication type:

Article

Pocketome: an encyclopedia of small-molecule binding sites in 4D.

Published in:

Nucleic Acids Research, 2012, p. D535, doi. 10.1093/nar/gkr825

By:

Kufareva, Irina;
Ilatovskiy, Andrey V.;
Abagyan, Ruben

Publication type:

Article

Predicting pK<sub>a</sub> values from EEM atomic charges.

Published in:

Journal of Cheminformatics, 2013, v. 5, n. 1, p. 1, doi. 10.1186/1758-2946-5-18

By:

Vařeková, Radka Svobodová;
Geidl, Stanislav;
Ionescu, Crina-Maria;
Skřehota, Ondřej;
Bouchal, Tomáš;
Sehnal, David;
Abagyan, Ruben;
Koča, Jaroslav

Publication type:

Article

Nilotinib, an approved leukemia drug, inhibits smoothened signaling in Hedgehog-dependent medulloblastoma.

Published in:

PLoS ONE, 2019, v. 14, n. 9, p. 1, doi. 10.1371/journal.pone.0214901

By:

Chahal, Kirti Kandhwal;
Li, Jie;
Kufareva, Irina;
Parle, Milind;
Durden, Donald L.;
Wechsler-Reya, Robert J.;
Chen, Clark C.;
Abagyan, Ruben

Publication type:

Article

Crosslinking-guided geometry of a complete CXC receptor-chemokine complex and the basis of chemokine subfamily selectivity.

Published in:

PLoS Biology, 2020, v. 18, n. 4, p. 1, doi. 10.1371/journal.pbio.3000656

By:

Ngo, Tony;
Stephens, Bryan S.;
Gustavsson, Martin;
Holden, Lauren G.;
Abagyan, Ruben;
Handel, Tracy M.;
Kufareva, Irina

Publication type:

Article

Population scale retrospective analysis reveals distinctive antidepressant and anxiolytic effects of diclofenac, ketoprofen and naproxen in patients with pain.

Published in:

PLoS ONE, 2018, v. 13, n. 4, p. 1, doi. 10.1371/journal.pone.0195521

By:

Makunts, Tigran;
Cohen, Isaac V.;
Lee, Kelly C.;
Abagyan, Ruben

Publication type:

Article

Mapping spatial approximations between the amino terminus of secretin and each of the extracellular loops of its receptor using cysteine trapping.

Published in:

FASEB Journal, 2012, v. 26, n. 12, p. 5092, doi. 10.1096/fj.12-212399

By:

Maoqing Dong;
Xiequn Xu;
Ball, Alicja M.;
Makhoul, Joshua A.;
Lam, Polo C.-H.;
Pinon, Delia I.;
Orry, Andrew;
Sexton, Patrick M.;
Abagyan, Ruben;
Miller, Laurence J.

Publication type:

Article

A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE).

Published in:

FASEB Journal, 2008, v. 22, p. 333, doi. 10.1096/fasebj.22.2_supplement.333

By:

Bottegoni, Giovanni;
Kufareva, Irina;
Totrov, Maxim;
Abagyan, Ruben

Publication type:

Article

Probing the Activator Specificity of Rhodospirillum rubrum ADPGlucose Pyrophosphorylase.

Published in:

FASEB Journal, 2007, v. 21, n. 6, p. A1018, doi. 10.1096/fasebj.21.6.a1018-a

By:

Wiig, Jared;
Doshi, Dhaval;
Amer, Adeel;
Amin, Chintan;
Charoensak, Piranid;
Orry, Andrew;
Abagyan, Ruben;
Meyer, Christopher R.

Publication type:

Article

Characterization of Thermus thermophilus ADPGlucose Pyrophosphorylase.

Published in:

FASEB Journal, 2007, v. 21, n. 5, p. A642, doi. 10.1096/fasebj.21.5.a642-d

By:

Gonzalez, Jacob;
Watanabe, Go;
Orry, Andrew;
Abagyan, Ruben;
Meyer, Christopher R.

Publication type:

Article

Homology modeling and ligand docking of Mitogen-activated protein kinase-activated protein kinase 5 (MK5).

Published in:

Theoretical Biology & Medical Modelling, 2013, v. 10, n. 1, p. 1, doi. 10.1186/1742-4682-10-56

By:

Lindin, Inger;
Yimingjiang Wuxiuer;
Kufareva, Irina;
Abagyan, Ruben;
Moens, Ugo;
Sylte, Ingebrigt;
Ravna, Aina Westrheim

Publication type:

Article

Match-Only Integral Distribution (MOID) Algorithm for high-density oligonucleotide array analysis.

Published in:

BMC Bioinformatics, 2002, v. 3, p. 3, doi. 10.1186/1471-2105-3-3

By:

Yingyao Zhou;
Abagyan, Ruben

Publication type:

Article

Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches.

Published in:

Journal of Computer-Aided Molecular Design, 2007, v. 21, n. 10/11, p. 549, doi. 10.1007/s10822-007-9138-7

By:

Katritch, Vsevolod;
Byrd, Chelsea M.;
Tseitin, Vladimir;
Dongcheng Dai;
Raush, Eugene;
Totrov, Maxim;
Abagyan, Ruben;
Jordan, Robert;
Hruby, Dennis

Publication type:

Article

Surrogate data – a secure way to share corporate data.

Published in:

Journal of Computer-Aided Molecular Design, 2005, v. 19, n. 9/10, p. 749, doi. 10.1007/s10822-005-9013-3

By:

Tetko, Igor V.;
Abagyan, Ruben;
Oprea, Tudor I.

Publication type:

Article

Comparative study of several algorithms for flexible ligand docking.

Published in:

Journal of Computer-Aided Molecular Design, 2003, v. 17, n. 11, p. 755, doi. 10.1023/B:JCAM.0000017496.76572.6f

By:

Bursulaya, Badry D.;
Totrov, Maxim;
Abagyan, Ruben;
Brooks III, Charles L.

Publication type:

Article

FRODOCK: a new approach for fast rotational protein–protein docking.

Published in:

Bioinformatics, 2009, v. 25, n. 19, p. 2544, doi. 10.1093/bioinformatics/btp447

By:

Garzon, José Ignacio;
Lopéz-Blanco, José Ramón;
Pons, Carles;
Kovacs, Julio;
Abagyan, Ruben;
Fernandez-Recio, Juan;
Chacon, Pablo

Publication type:

Article

DFprot: a webtool for predicting local chain deformability.

Published in:

Bioinformatics, 2007, v. 23, n. 7, p. 901, doi. 10.1093/bioinformatics/btm014

By:

José Ignacio Garzón;
Julio Kovacs;
Ruben Abagyan;
Pablo Chacón

Publication type:

Article

ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage.

Published in:

Bioinformatics, 2007, v. 23, n. 4, p. 427

By:

Julio Kovacs;
Ruben Abagyan;
Pablo Chacón

Publication type:

Article

Weighted quality estimates in machine learning.

Published in:

Bioinformatics, 2006, v. 22, n. 21, p. 2597, doi. 10.1093/bioinformatics/btl458

By:

Levon Budagyan;
Ruben Abagyan

Publication type:

Article

SAD—a normalized structural alignment database: improving sequence–structure alignments.

Published in:

Bioinformatics, 2004, v. 20, n. 15, p. 2333, doi. 10.1093/bioinformatics/bth244

By:

Brian Marsden;
Ruben Abagyan

Publication type:

Article

Mtor inhibitors associated with higher cardiovascular adverse events—A large population database analysis.

Published in:

Clinical Transplantation, 2021, v. 35, n. 4, p. 1, doi. 10.1111/ctr.14228

By:

Nguyen, Vi N.;
Abagyan, Ruben;
Tsunoda, Shirley M.

Publication type:

Article

Postmarketing safety surveillance data reveals protective effects of botulinum toxin injections against incident anxiety.

Published in:

Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-03713-x

By:

Wollmer, M. Axel;
Makunts, Tigran;
Krüger, Tillmann H. C.;
Abagyan, Ruben

Publication type:

Article

Common osteoporosis drug associated with increased rates of depression and anxiety.

Published in:

Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-03214-x

By:

Keshishi, Dro;
Makunts, Tigran;
Abagyan, Ruben

Publication type:

Article

Myocarditis occurrence with cancer immunotherapy across indications in clinical trial and post-marketing data.

Published in:

Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-96467-5

By:

Makunts, Tigran;
Saunders, Ila M.;
Cohen, Isaac V.;
Li, Mengxing;
Moumedjian, Talar;
Issa, Masara A.;
Burkhart, Keith;
Lee, Peter;
Patel, Sandip Pravin;
Abagyan, Ruben

Publication type:

Article

Identifying ligands at orphan GPCRs: current status using structure-based approaches.

Published in:

2016

By:

Ngo, Tony;
Kufareva, Irina;
Coleman, James LJ;
Graham, Robert M;
Abagyan, Ruben;
Smith, Nicola J

Publication type:

journal article

The anthelmintic praziquantel is a human serotoninergic G-protein-coupled receptor ligand.

Published in:

Nature Communications, 2017, v. 8, n. 1, p. 1, doi. 10.1038/s41467-017-02084-0

By:

Chan, John D.;
Gunaratne, Gihan S.;
Yang Yang;
Marchant, Jonathan S.;
Cupit, Pauline M.;
Abagyan, Ruben;
McCorvy, John D.;
Roth, Bryan L.;
Stoltz, Kristen;
Dosa, Peter I.;
Webb, Thomas R.;
Cunningham, Charles

Publication type:

Article

CYP51 is an essential drug target for the treatment of primary amoebic meningoencephalitis (PAM).

Published in:

PLoS Neglected Tropical Diseases, 2017, v. 11, n. 12, p. 1, doi. 10.1371/journal.pntd.0006104

By:

Debnath, Anjan;
Jennings, Gareth;
Aksenov, Alexander;
Luth, Madeline R.;
Abagyan, Ruben;
McKerrow, James H.;
Podust, Larissa M.;
Calvet, Claudia M.;
Zhou, Wenxu;
Nes, W. David

Publication type:

Article

Phenotypic, chemical and functional characterization of cyclic nucleotide phosphodiesterase 4 (PDE4) as a potential anthelmintic drug target.

Published in:

PLoS Neglected Tropical Diseases, 2017, v. 11, n. 7, p. 1, doi. 10.1371/journal.pntd.0005680

By:

Long, Thavy;
Rojo-Arreola, Liliana;
Shi, Da;
El-Sakkary, Nelly;
Jarnagin, Kurt;
Rock, Fernando;
Meewan, Maliwan;
Jr.Rascón, Alberto A.;
Lin, Lin;
Cunningham, Katherine A.;
Lemieux, George A.;
Podust, Larissa;
Abagyan, Ruben;
Ashrafi, Kaveh;
McKerrow, James H.;
Caffrey, Conor R.

Publication type:

Article

Structure-based Design, Synthesis, and Biological Evaluation of Isatin Derivatives as Potential Glycosyltransferase Inhibitors.

Published in:

Chemical Biology & Drug Design, 2014, v. 84, n. 6, p. 685, doi. 10.1111/cbdd.12361

By:

Wang, Yong;
Chan, Fung ‐ Yi;
Sun, Ning;
Lui, Hok ‐ Kiu;
So, Pui ‐ Kin;
Yan, Siu ‐ Cheong;
Chan, Kin ‐ Fai;
Chiou, Jiachi;
Chen, Sheng;
Abagyan, Ruben;
Leung, Yun ‐ Chung;
Wong, Kwok ‐ Yin

Publication type:

Article

Synthesis, Antidepressant Evaluation and Docking Studies of Long-Chain Alkylnitroquipazines as Serotonin Transporter Inhibitors.

Published in:

Chemical Biology & Drug Design, 2013, v. 81, n. 6, p. 695, doi. 10.1111/cbdd.12116

By:

Gabrielsen, Mari;
Wołosewicz, Karol;
Zawadzka, Anna;
Kossakowski, Jerzy;
Nowak, Gabriel;
Wolak, Małgorzata;
Stachowicz, Katarzyna;
Siwek, Agata;
Ravna, Aina W.;
Kufareva, Irina;
Kozerski, Lech;
Bednarek, Elżbieta;
Sitkowski, Jerzy;
Bocian, Wojciech;
Abagyan, Ruben;
Bojarski, Andrzej J.;
Sylte, Ingebrigt;
Chilmonczyk, Zdzisław

Publication type:

Article

A Metal-Based Inhibitor of Tumor Necrosis Factor-α.

Published in:

Angewandte Chemie, 2012, v. 124, n. 36, p. 9144, doi. 10.1002/ange.201202937

By:

Leung, Chung-Hang;
Zhong, Hai-Jing;
Yang, Hui;
Cheng, Zhen;
Chan, Daniel Shiu-Hin;
Ma, Victor Pui-Yan;
Abagyan, Ruben;
Wong, Chun-Yuen;
Ma, Dik-Lung

Publication type:

Article

Structure-Based Discovery of Natural-Product-like TNF-α Inhibitors.

Published in:

Angewandte Chemie, 2010, v. 122, n. 16, p. 2922, doi. 10.1002/ange.200907360

By:

Chan, Daniel Shiu-Hin;
Lee, Ho-Man;
Yang, Fang;
Che, Chi-Ming;
Wong, Catherine C. L.;
Abagyan, Ruben;
Leung, Chung-Hang;
Ma, Dik-Lung

Publication type:

Article

Druggable exosites of the human kino-pocketome.

Published in:

Journal of Computer-Aided Molecular Design, 2020, v. 34, n. 3, p. 219, doi. 10.1007/s10822-019-00276-y

By:

Nicola, George;
Kufareva, Irina;
Ilatovskiy, Andrey V.;
Abagyan, Ruben

Publication type:

Article

Macrocycle modeling in ICM: benchmarking and evaluation in D3R Grand Challenge 4.

Published in:

Journal of Computer-Aided Molecular Design, 2019, v. 33, n. 12, p. 1057, doi. 10.1007/s10822-019-00225-9

By:

Lam, Polo C.-H.;
Abagyan, Ruben;
Totrov, Maxim

Publication type:

Article

Hybrid receptor structure/ligand-based docking and activity prediction in ICM: development and evaluation in D3R Grand Challenge 3.

Published in:

Journal of Computer-Aided Molecular Design, 2019, v. 33, n. 1, p. 35, doi. 10.1007/s10822-018-0139-5

By:

Lam, Polo C.-H.;
Abagyan, Ruben;
Totrov, Maxim

Publication type:

Article

Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach.

Published in:

Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 187, doi. 10.1007/s10822-017-0058-x

By:

Lam, Polo C.-H.;
Abagyan, Ruben;
Totrov, Maxim

Publication type:

Article

Docking and scoring with ICM: the benchmarking results and strategies for improvement.

Published in:

Journal of Computer-Aided Molecular Design, 2012, v. 26, n. 6, p. 675, doi. 10.1007/s10822-012-9547-0

By:

Neves, Marco;
Totrov, Maxim;
Abagyan, Ruben

Publication type:

Article

Computational chemistry in 25 years.

Published in:

Journal of Computer-Aided Molecular Design, 2012, v. 26, n. 1, p. 9, doi. 10.1007/s10822-011-9516-z

By:

Abagyan, Ruben

Publication type:

Article

Efficient molecular mechanics simulations of the folding, orientation, and assembly of peptides in lipid bilayers using an implicit atomic solvation model.

Published in:

Journal of Computer-Aided Molecular Design, 2011, v. 25, n. 10, p. 895, doi. 10.1007/s10822-011-9470-9

By:

Bordner, Andrew;
Zorman, Barry;
Abagyan, Ruben

Publication type:

Article

Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles.

Published in:

Journal of Computer-Aided Molecular Design, 2010, v. 24, n. 5, p. 459, doi. 10.1007/s10822-010-9362-4

By:

So-Jung Park;
Kufareva, Irina;
Abagyan, Ruben

Publication type:

Article

Identifying conformational changes of the β<sub>2</sub> adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators.

Published in:

Journal of Computer-Aided Molecular Design, 2009, v. 23, n. 5, p. 273, doi. 10.1007/s10822-008-9257-9

By:

Reynolds, Kimberly A.;
Katritch, Vsevolod;
Abagyan, Ruben

Publication type:

Article

A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE).

Published in:

Journal of Computer-Aided Molecular Design, 2008, v. 22, n. 5, p. 311, doi. 10.1007/s10822-008-9188-5

By:

Bottegoni, Giovanni;
Kufareva, Irina;
Totrov, Maxim;
Abagyan, Ruben

Publication type:

Article

The GPCR Network: a large-scale collaboration to determine human GPCR structure and function.

Published in:

Nature Reviews Drug Discovery, 2013, v. 12, n. 1, p. 25, doi. 10.1038/nrd3859

By:

Stevens, Raymond C.;
Cherezov, Vadim;
Katritch, Vsevolod;
Abagyan, Ruben;
Kuhn, Peter;
Rosen, Hugh;
Wüthrich, Kurt

Publication type:

Article

Performance-Driven and Cost-Efficient Convergence of Cloud and HPC: Evaluating MinIO and LustreFS.

Published in:

Baltic Journal of Modern Computing, 2025, v. 13, n. 1, p. 177, doi. 10.22364/bjmc.2025.13.1.10

By:

ASTSATRYAN, Hrachya;
BAGHDASARYAN, Hovhannes;
ABAGYAN, Ruben;
GRABSKI, Hovakim;
GRABSKA, Siranuysh

Publication type:

Article

A Thiazole Orange Derivative Targeting the Bacterial Protein FtsZ Shows Potent Antibacterial Activity.

Published in:

Frontiers in Microbiology, 2017, v. 8, p. 1, doi. 10.3389/fmicb.2017.00855

By:

Ning Sun;
Yu-Jing Lu;
Fung-Yi Chan;
Ruo-Lan Du;
Yuan-yuan Zheng;
Kun Zhang;
Lok-Yan So;
Ruben Abagyan;
Chao Zhuo;
Yun-Chung Leung;
Kwok-Yin Wong

Publication type:

Article

Flipping states: a few key residues decide the winning conformation of the only universally conserved transcription factor.

Published in:

Nucleic Acids Research, 2017, v. 45, n. 15, p. 8835, doi. 10.1093/nar/gkx523

By:

Da Shi;
Svetlov, Dmitri;
Abagyan, Ruben;
Artsimovitch, Irina

Publication type:

Article

Synthesis, Optimization, Antifungal Activity, Selectivity, and CYP51 Binding of New 2-Aryl-3-azolyl-1-indolyl-propan-2-ols.

Published in:

Pharmaceuticals (14248247), 2020, v. 13, n. 8, p. 186, doi. 10.3390/ph13080186

By:

Lebouvier, Nicolas;
Pagniez, Fabrice;
Na, Young Min;
Shi, Da;
Pinson, Patricia;
Marchivie, Mathieu;
Guillon, Jean;
Hakki, Tarek;
Bernhardt, Rita;
Yee, Sook Wah;
Simons, Claire;
Lézé, Marie-Pierre;
Hartmann, Rolf W.;
Mularoni, Angélique;
Le Baut, Guillaume;
Krimm, Isabelle;
Abagyan, Ruben;
Le Pape, Patrice;
Le Borgne, Marc

Publication type:

Article

Identifying Allosteric Small-Molecule Binding Sites of Inactive NS2B-NS3 Proteases of Pathogenic Flaviviridae.

Published in:

Viruses (1999-4915), 2025, v. 17, n. 1, p. 6, doi. 10.3390/v17010006

By:

Grabski, Hovakim;
Grabska, Siranuysh;
Abagyan, Ruben

Publication type:

Article

Allosteric Inhibitors of Zika Virus NS2B-NS3 Protease Targeting Protease in "Super-Open" Conformation.

Published in:

Viruses (1999-4915), 2023, v. 15, n. 5, p. 1106, doi. 10.3390/v15051106

By:

Meewan, Ittipat;
Shiryaev, Sergey A.;
Kattoula, Julius;
Huang, Chun-Teng;
Lin, Vivian;
Chuang, Chiao-Han;
Terskikh, Alexey V.;
Abagyan, Ruben

Publication type:

Article

High-throughput phenotypic screen identifies a new family of potent anti-amoebic compounds.

Published in:

PLoS ONE, 2023, v. 18, n. 5, p. 1, doi. 10.1371/journal.pone.0280232

By:

Sauvey, Conall;
Meewan, Ittipat;
Ehrenkaufer, Gretchen;
Blevitt, Jonathan;
Jackson, Paul;
Abagyan, Ruben

Publication type:

Article