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1

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

2

Biochemical Characterization of QPX7728, a New Ultra-Broad-Spectrum Beta-lactamase Inhibitor of Serine and Metallo-Beta-Lactamases

Tsivkovski, Ruslan, Totrov, Maxim, Lomovskaya, Olga

Journal:

Antimicrobial Agents and Chemotherapy

Year:

2020

File:

PDF, 1.40 MB

2020

3

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

4

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

5

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

6

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

7

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

8

Accurate and efficient generalized born model based on solvent accessibility: Derivation and application for LogP octanol/water prediction and flexible peptide docking

Journal:

Journal of Computational Chemistry

Year:

2004

Language:

english

File:

PDF, 354 KB

english, 2004

9

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

10

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

11

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

12

The use of the magnetic field effect for studying a chemiluminescent chemical reaction in aqueous solution. Reaction rate constants and lifetimes of intermediate molecules

Michael M. Triebel, Maxim M. Totrov, George E. Zorinyants, Eugene L. Frankevich

Journal:

Chemical Physics Letters

Year:

1993

Language:

english

File:

PDF, 467 KB

english, 1993

13

Phase-on-frequency characteristics of the magnetic field effect for studying the mechanism of the branching chemiluminescent reaction of luminol

Michael M. Triebel, Andrey K. Morozov, Maxim M. Totrov, George E. Zorinyants, Eugene L. Frankevich

Journal:

Chemical Physics Letters

Year:

1993

Language:

english

File:

PDF, 477 KB

english, 1993

14

Triazole-linked reduced amide isosteres: An approach for the fragment-based drug discovery of anti-Alzheimer’s BACE1 inhibitors

Christopher J. Monceaux, Chiho Hirata-Fukae, Polo C.-H. Lam, Maxim M. Totrov, Yasuji Matsuoka, Paul R. Carlier

Journal:

Bioorganic & Medicinal Chemistry Letters

Year:

2011

Language:

english

File:

PDF, 741 KB

english, 2011

15

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

16

Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 5.75 MB

english, 2011

17

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

18

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

19

Improving CAPRI predictions: Optimized desolvation for rigid-body docking

Juan Fernández-Recio, Ruben Abagyan, Maxim Totrov

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 214 KB

english, 2005

20

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

21

Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling

Yelena A. Arnautova, Ruben A. Abagyan, Maxim Totrov

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2011

Language:

english

File:

PDF, 815 KB

english, 2011

22

Homology modeling by the ICM method

Timothy Cardozo, Maxim Totrov, Ruben Abagyan

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1995

Language:

english

File:

PDF, 1.42 MB

english, 1995

23

Interactive JIMD articles using the iSee concept: turning a new page on structural biology data

Wen Hwa Lee, Wyatt W. Yue, Eugene Raush, Maxim Totrov, Ruben Abagyan, Udo Oppermann, Brian D. Marsden

Journal:

Journal of Inherited Metabolic Disease

Year:

2011

Language:

english

File:

PDF, 482 KB

english, 2011

24

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

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

Journal:

Journal of Computer-Aided Molecular Design

Year:

2007

Language:

english

File:

PDF, 554 KB

english, 2007

25

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

Giovanni Bottegoni, Irina Kufareva, Maxim Totrov, Ruben Abagyan

Journal:

Journal of Computer-Aided Molecular Design

Year:

2008

Language:

english

File:

PDF, 751 KB

english, 2008

26

Atomic Property Fields: Generalized 3D Pharmacophoric Potential for Automated Ligand Superposition, Pharmacophore Elucidation and 3D QSAR

Journal:

Chemical Biology & Drug Design

Year:

2008

Language:

english

File:

PDF, 1.10 MB

english, 2008

27

Waltzing transporters and 'the dance macabre' between humans and bacteria

Lomovskaya, Olga, Zgurskaya, Helen I., Totrov, Maxim, Watkins, William J.

Journal:

Nature Reviews Drug Discovery

Year:

2006

Language:

english

File:

PDF, 571 KB

english, 2006

28

Detailed ab initio prediction of lysozyme–antibody complex with 1.6 Å accuracy

Totrov, Maxim, Abagyan, Ruben

Journal:

Natural Structural Biology

Year:

1994

File:

PDF, 691 KB

1994

29

Conserved structural elements in the V3 crown of HIV-1 gp120

Jiang, Xunqing, Burke, Valicia, Totrov, Maxim, Williams, Constance, Cardozo, Timothy, Gorny, Miroslaw K, Zolla-Pazner, Susan, Kong, Xiang-Peng

Journal:

Nature Structural and Molecular Biology

Year:

2010

Language:

english

File:

PDF, 1.17 MB

english, 2010

30

Comparative study of several algorithms for flexible ligand docking

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

Journal:

Journal of Computer-Aided Molecular Design

Year:

2003

Language:

english

File:

PDF, 105 KB

english, 2003

31

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

Marco A. C. Neves, Maxim Totrov, Ruben Abagyan

Journal:

Journal of Computer-Aided Molecular Design

Year:

2012

Language:

english

File:

PDF, 794 KB

english, 2012

32

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

33

A Novel Class of Inhibitors of Peptide Deformylase Discovered through High-Throughput Screening and Virtual Ligand Screening

Howard, Michael H., Cenizal, Teodorica, Gutteridge, Steven, Hanna, Wayne S., Tao, Yong, Totrov, Maxim, Wittenbach, Vernon A., Zheng, Ya-jun

Journal:

Journal of Medicinal Chemistry

Year:

2004

Language:

english

File:

PDF, 185 KB

english, 2004

34

Towards a species-selective acetylcholinesterase inhibitor to control the mosquito vector of malaria, Anopheles gambiae

Paul R. Carlier, Troy D. Anderson, Dawn M. Wong, Danny C. Hsu, Joshua Hartsel, Ming Ma, Eric A. Wong, Ranginee Choudhury, Polo C.-H. Lam, Maxim M. Totrov, Jeffrey R. Bloomquist

Journal:

Chemico-Biological Interactions

Year:

2008

Language:

english

File:

PDF, 811 KB

english, 2008

35

Flexible ligand docking to multiple receptor conformations: a practical alternative

Maxim Totrov, Ruben Abagyan

Journal:

Current Opinion in Structural Biology

Year:

2008

Language:

english

File:

PDF, 1.49 MB

english, 2008

36

Structural Analysis of Human and Macaque mAbs 2909 and 2.5B: Implications for the Configuration of the Quaternary Neutralizing Epitope of HIV-1 gp120

Brett Spurrier, Jared M. Sampson, Maxim Totrov, Huiguang Li, Timothy O'Neal, Constance Williams, James Robinson, Miroslaw K. Gorny, Susan Zolla-Pazner, Xiang-Peng Kong

Journal:

Year:

2011

Language:

english

File:

PDF, 1.84 MB

english, 2011

37

Disseminating structural genomics data to the public: from a data dump to an animated story

Ruben Abagyan, Wen Hwa Lee, Eugene Raush, Levon Budagyan, Maxim Totrov, Michael Sundstrom, Brian D. Marsden

Journal:

Trends in Biochemical Sciences

Year:

2006

Language:

english

File:

PDF, 251 KB

english, 2006

38

Structure-guided design and immunological characterization of immunogens presenting the HIV-1 gp120 V3 loop on a CTB scaffold

Maxim Totrov, Xunqing Jiang, Xiang-Peng Kong, Sandra Cohen, Chavdar Krachmarov, Aidy Salomon, Constance Williams, Michael S. Seaman, Timothy Cardozo, Miroslaw K. Gorny, Shixia Wang, Shan Lu, Abraham P

Journal:

Year:

2010

Language:

english

File:

PDF, 1.45 MB

english, 2010

39

Corrigendum to “Structure-guided design and immunological characterization of immunogens presenting the HIV-1 gp120 V3 loop on a CTB scaffold” [Virology 351 (2010) 513–523]

Maxim Totrov, Xunqing Jiang, Xiang-Peng Kong, Sandra Cohen, Chavdar Krachmarov, Aidy Salomon, Constance Williams, Michael S. Seaman, Ruben Abagyan, Timothy Cardozo, Miroslaw K. Gorny, Shixia Wang, Sha

Journal:

Year:

2011

Language:

english

File:

PDF, 94 KB

english, 2011

40

Expression of the Adenovirus Receptor and Its Interaction with the Fiber Knob

Richard P. Tomko, Clas B. Johansson, Maxim Totrov, Ruben Abagyan, Jonas Frisén, Lennart Philipson

Journal:

Experimental Cell Research

Year:

2000

Language:

english

File:

PDF, 303 KB

english, 2000

41

Biased Probability Monte Carlo Conformational Searches and Electrostatic Calculations for Peptides and Proteins

Ruben Abagyan, Maxim Totrov

Journal:

Journal of Molecular Biology

Year:

1994

File:

PDF, 1.26 MB

1994

42

The Hydration of Globular Proteins as Derived from Volume and Compressibility Measurements: Cross Correlating Thermodynamic and Structural Data

Tigran V. Chalikian, Maxim Totrov, Ruben Abagyan, Kenneth J. Breslauer

Journal:

Journal of Molecular Biology

Year:

1996

Language:

english

File:

PDF, 474 KB

english, 1996

43

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

44

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

45

Re-engineering aryl methylcarbamates to confer high selectivity for inhibition of Anopheles gambiae versus human acetylcholinesterase

Joshua A. Hartsel, Dawn M. Wong, James M. Mutunga, Ming Ma, Troy D. Anderson, Ania Wysinski, Rafique Islam, Eric A. Wong, Sally L. Paulson, Jianyong Li, Polo C.H. Lam, Maxim M. Totrov, Jeffrey R. Bloo

Journal:

Bioorganic & Medicinal Chemistry Letters

Year:

2012

Language:

english

File:

PDF, 662 KB

english, 2012

46

Identification of Protein–Protein Interaction Sites from Docking Energy Landscapes

Juan Fernández-Recio, Maxim Totrov, Ruben Abagyan

Journal:

Journal of Molecular Biology

Year:

2004

Language:

english

File:

PDF, 6.46 MB

english, 2004

47

Four-Dimensional Docking: A Fast and Accurate Account of Discrete Receptor Flexibility in Ligand Docking

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

Journal:

Journal of Medicinal Chemistry

Year:

2009

Language:

english

File:

PDF, 1.75 MB

english, 2009

48

NEUROTOXICOLOGY OF bis ( n )-TACRINES ON Blattella germanica AND Drosophila melanogaster ACETYLCHOLINESTERASE

Mutunga, James M., Boina, Dhana Raj, Anderson, Troy D., Bloomquist, Jeffrey R., Carlier, Paul R., Wong, Dawn M., Lam, Polo C.-H., Totrov, Maxim. M.

Journal:

Archives of Insect Biochemistry and Physiology

Year:

2013

Language:

english

File:

PDF, 686 KB

english, 2013

49

Corrigendum to “Re-engineering aryl methylcarbamates to confer high selectivity for inhibition of Anopheles gambiae versus human acetylcholinesterase” [Bioorg. Med. Chem. Lett. 22 (2012) 4593–4598]

Hartsel, Joshua A., Wong, Dawn M., Mutunga, James M., Ma, Ming, Anderson, Troy D., Wysinski, Ania, Islam, Rafique, Wong, Eric A., Paulson, Sally L., Li, Jianyong, Lam, Polo C.H., Totrov, Maxim, Bloomq

Journal:

Bioorganic & Medicinal Chemistry Letters

Year:

2013

Language:

english

File:

PDF, 190 KB

english, 2013

50

Aryl methylcarbamates: Potency and selectivity towards wild-type and carbamate-insensitive (G119S) Anopheles gambiae acetylcholinesterase, and toxicity to G3 strain An. gambiae

Wong, Dawn M., Li, Jianyong, Lam, Polo C.H., Hartsel, Joshua A., Mutunga, James M., Totrov, Maxim, Bloomquist, Jeffrey R., Carlier, Paul R.

Journal:

Chemico-Biological Interactions

Year:

2013

Language:

english

File:

PDF, 534 KB

english, 2013

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