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1

[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

2

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

3

Problems of secondary gamma radiation in reactor shields

A. A. Abagyan, T. A. Germogenova, A. A. Dubinin, V. I. Zhuravlev, V. A. Klimanov, E. I. Kostin, V. P. Mashkovich, V. K. Sakharov, V. A. Utkin

Journal:

Year:

1975

Language:

english

File:

PDF, 370 KB

english, 1975

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

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

6

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

7

Operating experience with nuclear power plants and current tasks in Russia

A. A. Abagyan, B. Ya. Berezin, V. M. Vitkov, S. K. Morozov

Journal:

Year:

1993

Language:

english

File:

PDF, 386 KB

english, 1993

8

Nuclear power in the USSR

A. A. Abagyan, G. I. Biryukov, S. V. Bryunin, B. V. Budylin, L. A. Buldakov, N. I. Ermakov, V. A. Ivanov, L. A. Kochetkov, A. A. Lapshin, A. S. Polyakov, N. N. Ponomarev-Stepnoi, O. B. Samoilov, V. A.

Journal:

Year:

1990

Language:

english

File:

PDF, 1.30 MB

english, 1990

9

Thermodynamic and kinetic aspects of a single-reactor synthesis of 5-amino-3-methyl-1,2,4-triazole hydrochloride from aminoguanidine and acetic acid

E. V. Tarasova, V. M. Chernyshev, A. V. Chernysheva, R. S. Abagyan

Journal:

Russian Journal of Applied Chemistry

Year:

2011

Language:

english

File:

PDF, 189 KB

english, 2011

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

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

12

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

13

GPCR agonist binding revealed by modeling and crystallography

Vsevolod Katritch, Ruben Abagyan

Journal:

Trends in Pharmacological Sciences

Year:

2011

Language:

english

File:

PDF, 1.01 MB

english, 2011

14

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

15

Direct Derivation of van der Waals Force Field Parameters from Quantum Mechanical Interaction Energies

Bordner, A. J., Cavasotto, C. N., Abagyan, R. A.

Journal:

Journal of Physical Chemistry B

Year:

2003

Language:

english

File:

PDF, 79 KB

english, 2003

16

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

17

REVCOM: a robust Bayesian method for evolutionary rate estimation

Bordner, A. J., Abagyan, R.

Journal:

Year:

2005

Language:

english

File:

PDF, 177 KB

english, 2005

18

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

19

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

20

Motor-Evoked Potentials of the Abductor Hallucis Muscle and Their Relationship with Foot Arch Functional Anatomy

Mayorga, Tyrone, Giokas, Erato, Abagyan, Anaida, Patel, Dhaval, Sarraf, Yasmin, Paula, Michael, Chusid, Eileen, D'antoni, Anthony, Battaglia, Fortunato

Journal:

Journal of the American Podiatric Medical Association

Year:

2017

Language:

english

File:

PDF, 320 KB

english, 2017

21

Flexible protein–ligand docking by global energy optimization in internal coordinates

Totrov, Maxim, Abagyan, Ruben

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1997

Language:

english

File:

PDF, 352 KB

english, 1997

22

Homology modeling with internal coordinate mechanics: Deformation zone mapping and improvements of models via conformational search

Ruben Abagyan, Serge Batalov, Timothy Cardozo, Maxim Totrov, Jeremy Webber, Yingyao Zhou

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1997

Language:

english

File:

PDF, 602 KB

english, 1997

23

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

24

Prediction of the binding energy for small molecules, peptides and proteins

Matthieu Schapira, Maxim Totrov, Ruben Abagyan

Journal:

Journal of Molecular Recognition

Year:

1999

Language:

english

File:

PDF, 262 KB

english, 1999

25

Modeling, mutagenesis, and structural studies on the fully conserved phosphate-binding loop (Loop 8) of triosephosphate isomerase: Toward a new substrate specificity

Brian V. Norledge, Anne M. Lambeir, Ruben A. Abagyan, Antje Rottmann, Anna M. Fernandez, Vladimir V. Filimonov, Martin G. Peter, Rik K. Wierenga

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2001

Language:

english

File:

PDF, 257 KB

english, 2001

26

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

Maxim Totrov, Ruben Abagyan

Journal:

Year:

2001

Language:

english

File:

PDF, 412 KB

english, 2001

27

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

28

Conformational analysis of polytripeptides (Gly-Pro-Ala)n, (Gly-Ala-Hyp)n, and (Gly-Ala-Ala)n in connection with the problem of collagen structure

V. G. Tumanyan, R. A. Abagyan, N. G. Esipova

Journal:

Year:

1984

Language:

english

File:

PDF, 665 KB

english, 1984

29

Structure of the hydration shells of oligo(dA-dT)·oligo(dA-dT) and oligo(dA)·oligo(dT) tracts in B-type conformation on the basis of Monte Carlo calculations

F. Eisenhaber, V. G. Tumanyan, R. A. Abagyan

Journal:

Year:

1990

Language:

english

File:

PDF, 1.49 MB

english, 1990

30

Stabilization of G-Quadruplex DNA with Platinum(II) Schiff Base Complexes: Luminescent Probe and Down-Regulation of c-myc Oncogene Expression

Peng Wu, Dik-Lung Ma, Chung-Hang Leung, Siu-Cheong Yan, Nianyong Zhu, R. Abagyan, Chi-Ming Che

Journal:

Chemistry - A European Journal

Year:

2009

Language:

english

File:

PDF, 863 KB

english, 2009

31

Discovery of a Drug-Like G-Quadruplex Binding Ligand by High-Throughput Docking

Dik-Lung Ma, Tat-Shing Lai, Fung-Yi Chan, Wai-Hong Chung, R. Abagyan, Yun-Chung Leung, Kwok-Yin Wong

Journal:

Year:

2008

Language:

english

File:

PDF, 332 KB

english, 2008

32

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

33

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

Ruben Abagyan, Maxim Totrov, Dmitry Kuznetsov

Journal:

Journal of Computational Chemistry

Year:

1994

Language:

english

File:

PDF, 1.62 MB

english, 1994

34

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

Maxim Totrov, Ruben Abagyan

Journal:

Journal of Computational Chemistry

Year:

1994

Language:

english

File:

PDF, 949 KB

english, 1994

35

Analysis of full and partial agonists binding to β2-adrenergic receptor suggests a role of transmembrane helix V in agonist-specific conformational changes

Vsevolod Katritch, Kimberly A. Reynolds, Vadim Cherezov, Michael A. Hanson, Christopher B. Roth, Mark Yeager, Ruben Abagyan

Journal:

Journal of Molecular Recognition

Year:

2009

Language:

english

File:

PDF, 746 KB

english, 2009

36

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

37

Derivation and testing of explicit equations of motion for polymers described by internal coordinates

A.K Mazur, V.E Dorofeev, R.A Abagyan

Journal:

Journal of Computational Physics

Year:

1991

Language:

english

File:

PDF, 642 KB

english, 1991

38

Conformational energy derivatives for polypeptides with flexible proline rings

R.A. Abagyan, A.K. Mazur

Journal:

Computers & Chemistry

Year:

1990

Language:

english

File:

PDF, 719 KB

english, 1990

39

A technique for identifying atoms from a screen image

D.A. Kuznetsov, R.A. Abagyan

Journal:

Journal of Molecular Graphics

Year:

1993

Language:

english

File:

PDF, 349 KB

english, 1993

40

Long chain amines and long chain ammonium salts as novel inhibitors of dynamin GTPase activity

Timothy A. Hill, Luke R. Odell, Annie Quan, Ruben Abagyan, Gemma Ferguson, Phillip J. Robinson, Adam McCluskey

Journal:

Bioorganic & Medicinal Chemistry Letters

Year:

2004

Language:

english

File:

PDF, 260 KB

english, 2004

41

In silico identification of novel EGFR inhibitors with antiproliferative activity against cancer cells

Claudio N. Cavasotto, María A. Ortiz, Ruben A. Abagyan, F. Javier Piedrafita

Journal:

Bioorganic & Medicinal Chemistry Letters

Year:

2006

Language:

english

File:

PDF, 418 KB

english, 2006

42

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

43

Estimating local backbone structural deviation in homology models

Timothy Cardozo, Serge Batalov, Ruben Abagyan

Journal:

Computers & Chemistry

Year:

2000

Language:

english

File:

PDF, 1.85 MB

english, 2000

44

High-throughput docking for lead generation

Ruben Abagyan, Maxim Totrov

Journal:

Current Opinion in Chemical Biology

Year:

2001

Language:

english

File:

PDF, 84 KB

english, 2001

45

The transthyretin-related protein family

Therese Eneqvist, Erik Lundberg, Lars Nilsson, Ruben Abagyan, A. Elisabeth Sauer-Eriksson

Journal:

Year:

2003

Language:

english

File:

PDF, 823 KB

english, 2003

46

In silico discovery of novel Retinoic Acid Receptor agonist structures

Matthieu Schapira, Bruce M Raaka, Herbert H Samuels, Ruben Abagyan

Journal:

BMC Structural Biology

Year:

2001

Language:

english

File:

PDF, 1.18 MB

english, 2001

47

Structural model of nicotinic acetylcholine receptor isotypes bound to acetylcholine and nicotine

Matthieu Schapira, Ruben Abagyan, Maxim Totrov

Journal:

BMC Structural Biology

Year:

2002

Language:

english

File:

PDF, 1.12 MB

english, 2002

48

Evaluating the energetics of empty cavities and internal mutations in proteins

Alexander A. Rashin, Bella H. Rashin, Annita Rashin, Ruben Abagyan

Journal:

Protein Science

Year:

1997

Language:

english

File:

PDF, 2.74 MB

english, 1997

49

ICM-DISCO docking by global energy optimization with fully flexible side-chains

Juan Fernández-Recio, Maxim Totrov, Ruben Abagyan

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2003

Language:

english

File:

PDF, 445 KB

english, 2003

50

Structure-based identification of binding sites, native ligands and potential inhibitors for G-protein coupled receptors

Claudio N. Cavasotto, Andrew J.W. Orry, Ruben A. Abagyan

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2003

Language:

english

File:

PDF, 443 KB

english, 2003