Ruben Abagyan: search on Z-Library

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1

Cascade reactions leading to the mechanism of action of vinaxanthone and xanthofulvin, natural products that drive nerve repair

Eliasen, Anders M., Chin, Matthew R., Axelrod, Abram J., Abagyan, Ruben, Siegel, Dionicio

Journal:

Year:

2018

Language:

english

File:

PDF, 1.98 MB

english, 2018

2

[Methods in Molecular Biology] Homology Modeling Volume 857 || A Practical Introduction to Molecular Dynamics Simulations: Applications to Homology Modeling

Orry, Andrew J. W., Abagyan, Ruben

Year:

2012

Language:

english

File:

PDF, 1.36 MB

english, 2012

3

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

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

Journal:

Nature Reviews Drug Discovery

Year:

2012

Language:

english

File:

PDF, 960 KB

english, 2012

4

XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification

Want, Elizabeth J., O'Maille, Grace, Abagyan, Ruben, Siuzdak, Gary, Smith, Colin A.

Journal:

Analytical Chemistry

Year:

2006

Language:

english

File:

PDF, 439 KB

english, 2006

5

ALiBERO: Evolving a Team of Complementary Pocket Conformations Rather than a Single Leader

Rueda, Manuel, Totrov, Max, Abagyan, Ruben

Journal:

Journal of Chemical Information and Modeling

Year:

2012

Language:

english

File:

PDF, 2.48 MB

english, 2012

6

BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry

Rueda, Manuel, Orozco, Modesto, Totrov, Maxim, Abagyan, Ruben

Journal:

BMC Structural Biology

Year:

2013

Language:

english

File:

PDF, 739 KB

english, 2013

7

The protein folding problem: Finding a few minimums in a near infinite space

Patrick Argos, Ruben Abagyan

Journal:

Computers & Chemistry

Year:

1994

Language:

english

File:

PDF, 662 KB

english, 1994

8

Molecular mechanism of serotonin transporter inhibition elucidated by a new flexible docking protocol

Mari Gabrielsen, Rafał Kurczab, Aina W. Ravna, Irina Kufareva, Ruben Abagyan, Zdzisław Chilmonczyk, Andrzej J. Bojarski, Ingebrigt Sylte

Journal:

European Journal of Medicinal Chemistry

Year:

2012

Language:

english

File:

PDF, 2.04 MB

english, 2012

9

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

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

Journal:

Angewandte Chemie

Year:

2010

Language:

english

File:

PDF, 870 KB

english, 2010

10

Structure of the human histamine H1 receptor complex with doxepin

Shimamura, Tatsuro, Shiroishi, Mitsunori, Weyand, Simone, Tsujimoto, Hirokazu, Winter, Graeme, Katritch, Vsevolod, Abagyan, Ruben, Cherezov, Vadim, Liu, Wei, Han, Gye Won

Journal:

Year:

2011

Language:

english

File:

PDF, 1.46 MB

english, 2011

11

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

Ngo, Tony, Kufareva, Irina, Coleman, James L. J., Graham, Robert M., Abagyan, Ruben, Smith, Nicola J.

Journal:

British Journal of Pharmacology

Year:

2016

Language:

english

File:

PDF, 2.06 MB

english, 2016

12

Glossary of terms used in computational drug design, part II (IUPAC Recommendations 2015)

Martin, Yvonne C., Abagyan, Ruben, Ferenczy, György G., Gillet, Val J., Oprea, Tudor I., Ulander, Johan, Winkler, David, Zefirov, Nicolai S.

Journal:

Pure & Applied Chemistry

Year:

2016

Language:

english

File:

PDF, 615 KB

english, 2016

13

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

Vsevolod Katritch, Maxim Totrov, Ruben Abagyan

Journal:

Journal of Computational Chemistry

Year:

2003

Language:

english

File:

PDF, 805 KB

english, 2003

14

PIER: Protein interface recognition for structural proteomics

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

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2007

Language:

english

File:

PDF, 880 KB

english, 2007

15

The Contour-Buildup Algorithm to Calculate the Analytical Molecular Surface

Maxim Totrov, Ruben Abagyan

Journal:

Journal of Structural Biology

Year:

1996

Language:

english

File:

PDF, 484 KB

english, 1996

16

Stoichiometry and geometry of the CXC chemokine receptor 4 complex with CXC ligand 12: Molecular modeling and experimental validation

Kufareva, Irina, Stephens, Bryan S., Holden, Lauren G., Qin, Ling, Zhao, Chunxia, Kawamura, Tetsuya, Abagyan, Ruben, Handel, Tracy M.

Journal:

Proceedings of the National Academy of Sciences

Year:

2014

Language:

english

File:

PDF, 2.08 MB

english, 2014

17

[Methods in Molecular Biology] Homology Modeling Volume 857 || Loop Simulations

Orry, Andrew J. W., Abagyan, Ruben

Year:

2012

Language:

english

File:

PDF, 407 KB

english, 2012

18

How Does the Methodology of 3D Structure Preparation Influence the Quality of p K a Prediction?

Geidl, Stanislav, Svobodová Vařeková, Radka, Bendová, Veronika, Petrusek, Lukáš, Ionescu, Crina-Maria, Jurka, Zdeněk, Abagyan, Ruben, Koča, Jaroslav

Journal:

Journal of Chemical Information and Modeling

Year:

2015

Language:

english

File:

PDF, 530 KB

english, 2015

19

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

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

Journal:

Interdisciplinary Sciences: Computational Life Sciences

Year:

2019

File:

PDF, 2.45 MB

2019

20

Identification of four amoebicidal non-toxic compounds by a molecular docking screen of Naegleria fowleri sterol Δ8−Δ7-isomerase and phenotypic assays

Shi, Da, Chahal, Kirti Kandhwal, Oto, Patricia, Nothias, Louis-Félix, Debnath, Anjan, McKerrow, James H., Podust, Larissa M., Abagyan, Ruben

Journal:

ACS Infectious Diseases

Year:

2019

File:

PDF, 1.37 MB

2019

21

Discovery of Bioactive Small-Molecule Inhibitor of Poly ADP-Ribose Polymerase: Implications for Energy-Deficient Cells

Stephen M. Altmann, Andrey Muryshev, Elisa Fossale, Michele M. Maxwell, Francine N. Norflus, Jonathan Fox, Steven M. Hersch, Anne B. Young, Marcy E. MacDonald, Ruben Abagyan, Aleksey G. Kazantsev

Journal:

Chemistry & Biology

Year:

2006

Language:

english

File:

PDF, 349 KB

english, 2006

22

[Methods in Molecular Biology] Homology Modeling Volume 857 || Force Fields for Homology Modeling

Orry, Andrew J. W., Abagyan, Ruben

Year:

2012

Language:

english

File:

PDF, 354 KB

english, 2012

23

Contact area difference (CAD): a robust measure to evaluate accuracy of protein models

Ruben A. Abagyan, Maxim M. Totrov

Journal:

Journal of Molecular Biology

Year:

1997

Language:

english

File:

PDF, 402 KB

english, 1997

24

Structure based prediction of subtype-selectivity for adenosine receptor antagonists

Vsevolod Katritch, Irina Kufareva, Ruben Abagyan

Journal:

Neuropharmacology

Year:

2011

Language:

english

File:

PDF, 2.55 MB

english, 2011

25

The Pthaladyns : GTP Competitive Inhibitors of Dynamin I and II GTPase Derived from Virtual Screening

Odell, Luke R., Howan, Dian, Gordon, Christopher P., Robertson, Mark J., Chau, Ngoc, Mariana, Anna, Whiting, Ainslie E., Abagyan, Ruben, Daniel, James A., Gorgani, Nick N., Robinson, Phillip J., McClu

Journal:

Journal of Medicinal Chemistry

Year:

2010

Language:

english

File:

PDF, 2.64 MB

english, 2010

26

The Liganding of Glycolipid Transfer Protein Is Controlled by Glycolipid Acyl Structure

Malinina, Lucy, Malakhova, Margarita L., Kanack, Alex T., Lu, Min, Abagyan, Ruben, Brown, Rhoderick E., Patel, Dinshaw J.

Journal:

Year:

2006

Language:

english

File:

PDF, 706 KB

english, 2006

27

[ACM Press the third annual international conference - Lyon, France (1999.04.11-1999.04.14)] Proceedings of the third annual international conference on Computational molecular biology - RECOMB '99 - Derivation of sensitive discrimination potential for virtual ligand screening

Totrov, Maxim, Abagyan, Ruben

Year:

1999

Language:

english

File:

PDF, 547 KB

english, 1999

28

Use of Cysteine Trapping to Map Spatial Approximations between Residues Contributing to the Helix N-capping Motif of Secretin and Distinct Residues within Each of the Extracellular Loops of Its Receptor

Dong, Maoqing, Lam, Polo C.-H., Orry, Andrew, Sexton, Patrick M., Christopoulos, Arthur, Abagyan, Ruben, Miller, Laurence J.

Journal:

Journal of Biological Chemistry

Year:

2016

Language:

english

File:

PDF, 4.30 MB

english, 2016

29

[PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO. Proceedings of the 3rd Annual RECOMB Workshop - National University of Singapore, Singapore (17 – 18 July 2006)] Regulatory Genomics - COMPUTATIONAL STRUCTURAL PROTEOMICS AND INHIBITOR DISCOVERY

Language:

english

File:

PDF, 47 KB

english

30

Publisher Correction: Population scale data reveals the antidepressant effects of ketamine and other therapeutics approved for non-psychiatric indications

Cohen, Isaac V., Makunts, Tigran, Atayee, Rabia, Abagyan, Ruben

Journal:

Scientific Reports

Year:

2017

Language:

english

File:

PDF, 666 KB

english, 2017

31

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

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

Journal:

Nucleic Acids Research

Year:

2017

Language:

english

File:

PDF, 2.34 MB

english, 2017

32

A General Method for Site Specific Fluorescent Labeling of Recombinant Chemokines

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., Hand

Journal:

Year:

2014

Language:

english

File:

PDF, 5.40 MB

english, 2014

33

A new method for modeling large-scale rearrangements of protein domains

Vladimir Maiorov, Ruben Abagyan

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1997

Language:

english

File:

PDF, 353 KB

english, 1997

34

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

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

Journal:

Angewandte Chemie International Edition

Year:

2010

Language:

english

File:

PDF, 870 KB

english, 2010

35

Ab InitioFolding of Peptides by the Optimal-Bias Monte Carlo Minimization Procedure

Ruben A Abagyan, Maxim Totrov

Journal:

Journal of Computational Physics

Year:

1999

Language:

english

File:

PDF, 361 KB

english, 1999

36

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

Andrew J. Bordner, Barry Zorman, Ruben Abagyan

Journal:

Journal of Computer-Aided Molecular Design

Year:

2011

Language:

english

File:

PDF, 522 KB

english, 2011

37

Molecular basis of agonicity and antagonicity in the androgen receptor studied by molecular dynamics simulations

William H. Bisson, Ruben Abagyan, Claudio N. Cavasotto

Journal:

Journal of Molecular Graphics and Modelling

Year:

2008

Language:

english

File:

PDF, 770 KB

english, 2008

38

Soft protein–protein docking in internal coordinates

Juan Fernández-Recio, Maxim Totrov, Ruben Abagyan

Journal:

Protein Science

Year:

2002

Language:

english

File:

PDF, 999 KB

english, 2002

39

Energy strain in three-dimensional protein structures

Vladimir Maiorov, Ruben Abagyan

Journal:

Folding and Design

Year:

1998

Language:

english

File:

PDF, 265 KB

english, 1998

40

Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases

Claudio N. Cavasotto, Ruben A. Abagyan

Journal:

Journal of Molecular Biology

Year:

2004

Language:

english

File:

PDF, 1.44 MB

english, 2004

41

Sequence-Conserved and Antibody-Accessible Sites in the V1V2 Domain of HIV-1 gp120 Envelope Protein

Shmelkov, Evgeny, Grigoryan, Arsen, Krachmarov, Chavdar, Abagyan, Ruben, Cardozo, Timothy

Journal:

AIDS Research and Human Retroviruses

Year:

2014

Language:

english

File:

PDF, 834 KB

english, 2014

42

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

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

Journal:

Year:

2009

Language:

english

File:

PDF, 489 KB

english, 2009

43

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

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

Journal:

Journal of Computer-Aided Molecular Design

Year:

2019

Language:

english

File:

PDF, 4.28 MB

english, 2019

44

Elucidation of Protein-Protein Interactions Throughout E. coli Fatty Acid Biosynthesis

Bartholow, Thomas G., Sztain-Pedone, Terra, Patel, Ashay, Abagyan, Ruben, Burkart, Michael D.

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 48 KB

2020

45

Small Molecule Inhibitors of Dynamin I GTPase Activity: Development of Dimeric Tyrphostins

Graham, Mark E., McGeachie, Andrew B., Rusak, Jenny, Quan, Annie, Abagyan, Ruben, Scott, Janet L., Robinson, Phillip J., Hill, Timothy, Odell, Luke R., Edwards, Jennifer K.

Journal:

Journal of Medicinal Chemistry

Year:

2005

Language:

english

File:

PDF, 166 KB

english, 2005

46

Soft docking an L and a D peptide to an anticholera toxin antibody using internal coordinate mechanics

Rolf-Dietrich Stigler, Berit Hoffmann, Ruben Abagyan, Jens Schneider-Mergener

Journal:

Year:

1999

Language:

english

File:

PDF, 179 KB

english, 1999

47

Viral Infection Controlled by a Calcium-Dependent Lipid-Binding Module in ALIX

Bissig, Christin, Lenoir, Marc, Velluz, Marie-Claire, Kufareva, Irina, Abagyan, Ruben, Overduin, Michael, Gruenberg, Jean

Journal:

Developmental Cell

Year:

2013

Language:

english

File:

PDF, 2.00 MB

english, 2013

48

[Methods in Molecular Biology] Homology Modeling Volume 857 || Investigating Protein Variants Using Structural Calculation Techniques

Orry, Andrew J. W., Abagyan, Ruben

Year:

2012

Language:

english

File:

PDF, 316 KB

english, 2012

49

Identification of a New Class of FtsZ Inhibitors by Structure-Based Design and in Vitro Screening

Chan, Fung-Yi, Sun, Ning, Neves, Marco A. C., Lam, Polo Chun-Hung, Chung, Wai-Hong, Wong, Lai-King, Chow, Ho-Yin, Ma, Dik-Lung, Chan, Pak-Ho, Leung, Yun-Chung, Chan, Tak-Hang, Abagyan, Ruben, Wong, Kw

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 467 KB

english, 2013

50

Quantum mechanics approaches to drug research in the era of structural chemogenomics

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

Journal:

International Journal of Quantum Chemistry

Year:

2013

Language:

english

File:

PDF, 338 KB

english, 2013

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