Works by Abagyan, Ruben

Results: 130

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

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

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

Differential activities of maize plant elicitor peptides as mediators of immune signaling and herbivore resistance.

Published in:

Plant Journal, 2020, v. 104, n. 6, p. 1582, doi. 10.1111/tpj.15022

By:

Poretsky, Elly;
Dressano, Keini;
Weckwerth, Philipp;
Ruiz, Miguel;
Char, Si Nian;
Shi, Da;
Abagyan, Ruben;
Yang, Bing;
Huffaker, Alisa

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

ICFF: A new method to incorporate implicit flexibility into an internal coordinate force field.

Published in:

Journal of Computational Chemistry, 2003, v. 24, n. 2, p. 254, doi. 10.1002/jcc.10091

By:

Katritch, Vsevolod;
Totrov, Maxim;
Abagyan, Ruben

Publication type:

Article

Efficient parallelization of the energy, surface, and derivative calculations for internal coordinate mechanics.

Published in:

Journal of Computational Chemistry, 1994, v. 15, n. 10, p. 1105, doi. 10.1002/jcc.540151006

By:

Totrov, Maxim;
Abagyan, Ruben

Publication type:

Article

ICM-A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation.

Published in:

Journal of Computational Chemistry, 1994, v. 15, n. 5, p. 488, doi. 10.1002/jcc.540150503

By:

Abagyan, Ruben;
Totrov, Maxim;
Kuznetsov, Dmitry

Publication type:

Article

Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge.

Published in:

PLoS Computational Biology, 2021, v. 17, n. 9, p. 1, doi. 10.1371/journal.pcbi.1009302

By:

Xiong, Zhaoping;
Jeon, Minji;
Allaway, Robert J.;
Kang, Jaewoo;
Park, Donghyeon;
Lee, Jinhyuk;
Jeon, Hwisang;
Ko, Miyoung;
Jiang, Hualiang;
Zheng, Mingyue;
Tan, Aik Choon;
Guo, Xindi;
Dang, Kristen K.;
Tropsha, Alex;
Hecht, Chana;
Das, Tirtha K.;
Carlson, Heather A.;
Abagyan, Ruben;
Guinney, Justin;
Schlessinger, Avner

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

Rapid boundary element solvation electrostatics calculations in folding simulations: Successful folding of a 23-residue peptide.

Published in:

Biopolymers, 2001, v. 60, n. 2, p. 124, doi. 10.1002/1097-0282(2001)60:2<124::AID-BIP1008>3.0.CO;2-S

By:

Totrov, Maxim;
Abagyan, Ruben

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

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

Hepatic injury and hepatic failure adverse events in 3,4-methylene dioxymethamphetamine users reported to the FDA Adverse Event Reporting System.

Published in:

Frontiers in Psychiatry, 2024, p. 1, doi. 10.3389/fpsyt.2024.1414622

By:

Makunts, Tigran;
Abagyan, Ruben

Publication type:

Article

High-quality and universal empirical atomic charges for chemoinformatics applications.

Published in:

Journal of Cheminformatics, 2015, v. 7, p. 1, doi. 10.1186/s13321-015-0107-1

By:

Geidl, Stanislav;
Bouchal, Tomáš;
Raèek, Tomáš;
Vaøeková, Radka Svobodová;
Hejret, Václav;
Křenek, Aleš;
Abagyan, Ruben;
Koèa, Jaroslav

Publication type:

Article

Predicting pKa 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

Population Scale Retrospective Analysis Reveals Potential Risk of Cholestasis in Pregnant Women Taking Omeprazole, Lansoprazole, and Amoxicillin.

Published in:

Interdisciplinary Sciences: Computational Life Sciences, 2019, v. 11, n. 2, p. 273, doi. 10.1007/s12539-019-00335-w

By:

Zhang, Yonghong;
Shi, Da;
Abagyan, Ruben;
Dai, Weina;
Dong, Mingyang

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

Rational Design of Berberine-Based FtsZ Inhibitors with Broad-Spectrum Antibacterial Activity.

Published in:

PLoS ONE, 2014, v. 9, n. 5, p. 1, doi. 10.1371/journal.pone.0097514

By:

Sun, Ning;
Chan, Fung-Yi;
Lu, Yu-Jing;
Neves, Marco A. C.;
Lui, Hok-Kiu;
Wang, Yong;
Chow, Ka-Yan;
Chan, Kin-Fai;
Yan, Siu-Cheong;
Leung, Yun-Chung;
Abagyan, Ruben;
Chan, Tak-Hang;
Wong, Kwok-Yin

Publication type:

Article

A General Method for Site Specific Fluorescent Labeling of Recombinant Chemokines.

Published in:

PLoS ONE, 2014, v. 9, n. 1, p. 1, doi. 10.1371/journal.pone.0081454

By:

Kawamura, Tetsuya;
Stephens, Bryan;
Qin, Ling;
Yin, Xin;
Dores, Michael R.;
Smith, Thomas H.;
Grimsey, Neil;
Abagyan, Ruben;
Trejo, JoAnn;
Kufareva, Irina;
Fuster, Mark M.;
Salanga, Catherina L.;
Handel, Tracy M.

Publication type:

Article

Lapatinib-Binding Protein Kinases in the African Trypanosome: Identification of Cellular Targets for Kinase-Directed Chemical Scaffolds.

Published in:

PLoS ONE, 2013, v. 8, n. 2, p. 1, doi. 10.1371/journal.pone.0056150

By:

Katiyar, Samiksha;
Kufareva, Irina;
Behera, Ranjan;
Thomas, Sarah M.;
Ogata, Yuko;
Pollastri, Michael;
Abagyan, Ruben;
Mensa-Wilmot, Kojo

Publication type:

Article

Systematic Exploitation of Multiple Receptor Conformations for Virtual Ligand Screening.

Published in:

PLoS ONE, 2011, v. 6, n. 5, p. 1, doi. 10.1371/journal.pone.0018845

By:

Bottegoni, Giovanni;
Rocchia, Walter;
Rueda, Manuel;
Abagyan, Ruben;
Cavalli, Andrea

Publication type:

Article

SGC - Structural Biology and Human Health: A New Approach to Publishing Structural Biology Results.

Published in:

2009

By:

Wen Hwa Lee;
Atienza-Herrero, Julián;
Abagyan, Ruben;
Marsden, Brian D.

Publication type:

Opinion

A New Method for Publishing Three-Dimensional Content.

Published in:

2009

By:

Raush, Eugene;
Totrov, Max;
Marsden, Brian D.;
Abagyan, Ruben

Publication type:

Abstract

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

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

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

Transcriptome and binding data indicate that citral inhibits single strand DNA‐binding proteins.

Published in:

Physiologia Plantarum, 2020, v. 169, n. 1, p. 99, doi. 10.1111/ppl.13055

By:

Graña, Elisa;
Díaz‐Tielas, Carla;
Sánchez‐Moreiras, Adela M.;
Reigosa, Manuel J.;
Celeiro, María;
Abagyan, Ruben;
Teijeira, Marta;
Duke, Mary V.;
Clerk, Tracy;
Pan, Zhiqiang;
Duke, Stephen O.

Publication type:

Article

Anti-TNF-α therapy induced psoriasis in rheumatoid arthritis patients according to FDA postmarketing surveillance data.

Published in:

Scientific Reports, 2023, v. 13, n. 1, p. 1, doi. 10.1038/s41598-023-37010-6

By:

Joulfayan, Haroutyun;
Makunts, Tigran;
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

Tyrosine Phosphorylation of the Gα-Interacting Protein GIV Promotes Activation of Phosphoinositide 3-Kinase During Cell Migration.

Published in:

Science Signaling, 2011, v. 4, n. 192, p. 1, doi. 10.1126/scisignal.2002049

By:

Lin, Changsheng;
Ear, Jason;
Pavlova, Yelena;
Mittal, Yash;
Kufareva, Irina;
Ghassemian, Majid;
Abagyan, Ruben;
Garcia-Marcos, Mikel;
Ghosh, Pradipta

Publication type:

Article

Multi-center screening of the Pathogen Box collection for schistosomiasis drug discovery.

Published in:

Parasites & Vectors, 2019, v. 12, n. 1, p. N.PAG, doi. 10.1186/s13071-019-3747-6

By:

Maccesi, Martina;
Aguiar, Pedro H. N.;
Pasche, Valérian;
Padilla, Melody;
Suzuki, Brian M.;
Montefusco, Sandro;
Abagyan, Ruben;
Keiser, Jennifer;
Mourão, Marina M.;
Caffrey, Conor R.

Publication type:

Article

Discovery of novel membrane binding structures and functions1.

Published in:

Biochemistry & Cell Biology, 2014, v. 92, n. 6, p. 555, doi. 10.1139/bcb-2014-0074

By:

Kufareva, Irina;
Lenoir, Marc;
Dancea, Felician;
Sridhar, Pooja;
Raush, Eugene;
Bissig, Christin;
Gruenberg, Jean;
Abagyan, Ruben;
Overduin, Michael

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

Membrane and Protein Interactions of the Pleckstrin Homology Domain Superfamily.

Published in:

Membranes, 2015, v. 5, n. 4, p. 646, doi. 10.3390/membranes5040646

By:

Lenoir, Marc;
Kufareva, Irina;
Abagyan, Ruben;
Overduin, Michael

Publication type:

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

Docking analysis of transient complexes: Interaction of ferredoxin-NADP+ reductase with ferredoxin and flavodoxin.

Published in:

Proteins, 2008, v. 72, n. 3, p. 848, doi. 10.1002/prot.21979

By:

Medina, Milagros;
Abagyan, Ruben;
Gómez-Moreno, Carlos;
Fernandez-Recio, Juan

Publication type:

Article

PIER: Protein interface recognition for structural proteomics.

Published in:

Proteins, 2007, v. 67, n. 2, p. 400, doi. 10.1002/prot.21233

By:

Kufareva, Irina;
Budagyan, Levon;
Raush, Eugene;
Totrov, Maxim;
Abagyan, Ruben

Publication type:

Article

Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes.

Published in:

Proteins, 2006, v. 63, n. 3, p. 512, doi. 10.1002/prot.20831

By:

Bordner, Andrew J.;
Abagyan, Ruben

Publication type:

Article

Statistical analysis and prediction of protein-protein interfaces.

Published in:

Proteins, 2005, v. 60, n. 3, p. 353, doi. 10.1002/prot.20433

By:

Bordner, Andrew J.;
Abagyan, Ruben

Publication type:

Article