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1

Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature

Oleg V. Tsodikov, M. Thomas Record Jr., Yuri V. Sergeev

Journal:

Journal of Computational Chemistry

Year:

2002

Language:

english

File:

PDF, 115 KB

english, 2002

2

Complete Asymptotic Solution of Cylindrical and Spherical Poisson−Boltzmann Equations at Experimental Salt Concentrations

Shkel, Irina A., Tsodikov, Oleg V., Record, M. Thomas

Journal:

Journal of Physical Chemistry B

Year:

2000

Language:

english

File:

PDF, 114 KB

english, 2000

3

Effects of structural modifications on the metal binding, anti-amyloid activity, and cholinesterase inhibitory activity of chalcones

Fosso Yatchang, Marina, LeVine, III, Harry, Green, Keith D, Tsodikov, Oleg, Garneau-Tsodikova, Sylvie

Journal:

Organic & Biomolecular Chemistry

Year:

2015

Language:

english

File:

PDF, 3.29 MB

english, 2015

4

Discovery and optimization of two Eis inhibitor families as kanamycin adjuvants against drug-resistant M. tuberculosis

Garzan, Atefeh, Willby, Melisa J., Green, Keith D., Tsodikov, Oleg V, Posey, James E., Garneau-Tsodikova, Sylvie

Journal:

ACS Medicinal Chemistry Letters

Year:

2016

Language:

english

File:

PDF, 356 KB

english, 2016

5

A nonradioactive high-throughput assay for screening and characterization of adenylation domains for nonribosomal peptide combinatorial biosynthesis

Thomas J. McQuade, Abbie D. Shallop, Anita Sheoran, James E. DelProposto, Oleg V. Tsodikov, Sylvie Garneau-Tsodikova

Journal:

Analytical Biochemistry

Year:

2009

Language:

english

File:

PDF, 438 KB

english, 2009

6

Exact and user-friendly kinetic analysis of the two-step rapid equilibrium Michaelis–Menten mechanism

Sylvie Garneau-Tsodikova, Irina A. Shkel, Oleg V. Tsodikov

Journal:

Analytical Biochemistry

Year:

2009

Language:

english

File:

PDF, 224 KB

english, 2009

7

An easy-to-use tool for planning and modeling a calorimetric titration

Tapan Biswas, Oleg V. Tsodikov

Journal:

Analytical Biochemistry

Year:

2010

Language:

english

File:

PDF, 241 KB

english, 2010

8

Hexameric ring structure of the N-terminal domain of Mycobacterium tuberculosis DnaB helicase

Tapan Biswas, Oleg V. Tsodikov

Journal:

Year:

2008

Language:

english

File:

PDF, 798 KB

english, 2008

9

Structural basis for the recruitment of ERCC1-XPF to nucleotide excision repair complexes by XPA

Tsodikov, Oleg V, Ivanov, Dmitri, Orelli, Barbara, Staresincic, Lidija, Shoshani, Ilana, Oberman, Robert, Schärer, Orlando D, Wagner, Gerhard, Ellenberger, Tom

Journal:

The EMBO Journal

Year:

2007

Language:

english

File:

PDF, 304 KB

english, 2007

10

The structural basis for substrate versatility of chloramphenicol acetyltransferase CATI

Tapan Biswas, Jacob L. Houghton, Sylvie Garneau-Tsodikova, Oleg V. Tsodikov

Journal:

Protein Science

Year:

2012

Language:

english

File:

PDF, 1.48 MB

english, 2012

11

Structural Insight into Serine Protease Rv3671c that Protects M. tuberculosis from Oxidative and Acidic Stress

Tapan Biswas, Jennifer Small, Omar Vandal, Toshiko Odaira, Haiteng Deng, Sabine Ehrt, Oleg V. Tsodikov

Journal:

Year:

2010

Language:

english

File:

PDF, 1.29 MB

english, 2010

12

Aminoglycoside Multiacetylating Activity of the Enhanced Intracellular Survival Protein from Mycobacterium smegmatis and Its Inhibition

Chen, Wenjing, Green, Keith D., Tsodikov, Oleg V., Garneau-Tsodikova, Sylvie

Journal:

Year:

2012

Language:

english

File:

PDF, 2.93 MB

english, 2012

13

Cooperative and Anticooperative Effects in Binding of the First and Second Plasmid OsymOperators to a LacI Tetramer: Evidence for Contributions of Non-operator DNA Binding by Wrapping and Looping

Mark M. Levandoski, Oleg V. Tsodikov, Diane E. Frank, Sonya E. Melcher, Ruth M. Saecker, Thomas M. Record Jr

Journal:

Journal of Molecular Biology

Year:

1996

Language:

english

File:

PDF, 624 KB

english, 1996

14

Thermodynamics of the interactions of Lac repressor with variants of the symmetric Lac operator: effects of converting a consensus site to a non-specific site

Diane E. Frank, Ruth M. Saecker, Jeffrey P. Bond, Michael W. Capp, Oleg V. Tsodikov, Sonya E. Melcher, Mark M. Levandoski, M.Thomas Record Jr

Journal:

Journal of Molecular Biology

Year:

1997

Language:

english

File:

PDF, 510 KB

english, 1997

15

Quantitative analysis of multiple-hit footprinting studies to characterize DNA conformational changes in protein-DNA complexes: application to DNA opening by Eσ70 RNA polymerase

Oleg V. Tsodikov, Maria L. Craig, Ruth M. Saecker, M.Thomas Record Jr

Journal:

Journal of Molecular Biology

Year:

1998

Language:

english

File:

PDF, 385 KB

english, 1998

16

DNA footprints of the two kinetically significant intermediates in formation of an RNA polymerase-promoter open complex: evidence that interactions with start site and downstream DNA induce sequential conformational changes in polymerase and DNA

Maria L. Craig, Oleg V. Tsodikov, Kristi L. McQuade, Peter E. Schlax Jr, Michael W. Capp, Ruth M. Saecker, M.Thomas Record Jr

Journal:

Journal of Molecular Biology

Year:

1998

Language:

english

File:

PDF, 494 KB

english, 1998

17

Quantitative analysis of the kinetics of end-dependent disassembly of RecA filaments from ssDNA

Tanya A. Arenson, Oleg V. Tsodikov, Michael M. Cox

Journal:

Journal of Molecular Biology

Year:

1999

Language:

english

File:

PDF, 229 KB

english, 1999

18

Wrapping of flanking non-operator DNA in lac repressor-operator complexes: implications for DNA looping

Oleg V. Tsodikov, Ruth M. Saecker, Sonya E. Melcher, Mark M. Levandoski, Diane E. Frank, Michael W. Capp, M.Thomas Record Jr

Journal:

Journal of Molecular Biology

Year:

1999

Language:

english

File:

PDF, 420 KB

english, 1999

19

Specific and non-specific interactions of integration host factor with DNA: thermodynamic evidence for disruption of multiple IHF surface salt-bridges coupled to DNA binding

Jill A. Holbrook, Oleg V. Tsodikov, Ruth M. Saecker, M.Thomas Record Jr

Journal:

Journal of Molecular Biology

Year:

2001

Language:

english

File:

PDF, 600 KB

english, 2001

20

A New Scaffold of an Old Protein Fold Ensures Binding to the Bisintercalator Thiocoraline

Tapan Biswas, Olga E. Zolova, Felipe Lombó, Fernando de la Calle, Jose A. Salas, Oleg V. Tsodikov, Sylvie Garneau-Tsodikova

Journal:

Journal of Molecular Biology

Year:

2010

Language:

english

File:

PDF, 1.76 MB

english, 2010

21

Structural and Thermodynamic Signatures of DNA Recognition by Mycobacterium tuberculosis DnaA

Oleg V. Tsodikov, Tapan Biswas

Journal:

Journal of Molecular Biology

Year:

2011

Language:

english

File:

PDF, 1.04 MB

english, 2011

22

A Flexible Interface between DNA Ligase and PCNA Supports Conformational Switching and Efficient Ligation of DNA

John M. Pascal, Oleg V. Tsodikov, Greg L. Hura, Wei Song, Elizabeth A. Cotner, Scott Classen, Alan E. Tomkinson, John A. Tainer, Tom Ellenberger

Journal:

Year:

2006

Language:

english

File:

PDF, 1.11 MB

english, 2006

23

Kinetic Studies and Structural Models of the Association of E. coli σ70 RNA Polymerase with the λPR Promoter: Large Scale Conformational Changes in Forming the Kinetically Significant Intermediates

Ruth M Saecker, Oleg V Tsodikov, Kristi L McQuade, Peter E Schlax Jr, Michael W Capp, M Thomas Record Jr

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 580 KB

english, 2002

24

An Insertion in the Catalytic Trigger Loop Gates the Secondary Channel of RNA Polymerase

Furman, Ran, Tsodikov, Oleg V., Wolf, Yuri I., Artsimovitch, Irina

Journal:

Journal of Molecular Biology

Year:

2013

Language:

english

File:

PDF, 2.94 MB

english, 2013

25

Analytic Binding Isotherms Describing Competitive Interactions of a Protein Ligand with Specific and Nonspecific Sites on the Same DNA Oligomer

Tsodikov, Oleg V., Holbrook, Jill A., Shkel, Irina A., Record, M. Thomas

Journal:

Biophysical Journal

Year:

2001

Language:

english

File:

PDF, 209 KB

english, 2001

26

General Method of Analysis of Kinetic Equations for Multistep Reversible Mechanisms in the Single-Exponential Regime: Application to Kinetics of Open Complex Formation between Eσ70 RNA Polymerase and λPR Promoter DNA

Tsodikov, Oleg V., Record, M. Thomas

Journal:

Biophysical Journal

Year:

1999

Language:

english

File:

PDF, 137 KB

english, 1999

27

DksA2, a zinc-independent structural analog of the transcription factor DksA

Furman, Ran, Biswas, Tapan, Danhart, Eric M., Foster, Mark P., Tsodikov, Oleg V., Artsimovitch, Irina

Journal:

Year:

2013

Language:

english

File:

PDF, 1.03 MB

english, 2013

28

Discovery of Inhibitors of Bacillus anthracis Primase DnaG

Biswas, Tapan, Green, Keith D., Garneau-Tsodikova, Sylvie, Tsodikov, Oleg V.

Journal:

Year:

2013

Language:

english

File:

PDF, 889 KB

english, 2013

29

Chemical and Structural Insights into the Regioversatility of the Aminoglycoside Acetyltransferase Eis

Houghton, Jacob L., Biswas, Tapan, Chen, Wenjing, Tsodikov, Oleg V., Garneau-Tsodikova, Sylvie

Journal:

Year:

2013

Language:

english

File:

PDF, 2.21 MB

english, 2013

30

Denaturant Probes Quantify the Preferential Burial of Amide Surface in Forming the Key Transition State and Early Intermediates in Protein Folding

Sengupta, Rituparna, Guinn, Emily J., Kontur, Wayne S., Tsodikov, Oleg V., Shkel, Irina, Record, M. Thomas

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 38 KB

english, 2014

31

DNA-Dependent ATPase Activity of Bacterial XPB Helicases

Biswas, Tapan, Pero, Jessica M., Joseph, Caleb G., Tsodikov, Oleg V.

Journal:

Year:

2009

Language:

english

File:

PDF, 1.49 MB

english, 2009

32

Antimycobacterial activity of DNA intercalator inhibitors of Mycobacterium tuberculosis primase DnaG

Gajadeera, Chathurada, Willby, Melisa J, Green, Keith D, Shaul, Pazit, Fridman, Micha, Garneau-Tsodikova, Sylvie, Posey, James E, Tsodikov, Oleg V

Journal:

The Journal of Antibiotics

Year:

2015

Language:

english

File:

PDF, 460 KB

english, 2015

33

2′,6′-Dihalostyrylanilines, Pyridines, and Pyrimidines for the Inhibition of the Catalytic Subunit of Methionine S-Adenosyltransferase-2

Sviripa, Vitaliy M., Zhang, Wen, Balia, Andrii G., Tsodikov, Oleg V., Nickell, Justin R., Gizard, Florence, Yu, Tianxin, Lee, Eun Y., Dwoskin, Linda P., Liu, Chunming, Watt, David S.

Journal:

Journal of Medicinal Chemistry

Year:

2014

Language:

english

File:

PDF, 650 KB

english, 2014

34

Quantifying Additive Interactions of the Osmolyte Proline with Individual Functional Groups of Proteins: Comparisons with Urea and Glycine Betaine, Interpretation of m -Values

Diehl, Roger C., Guinn, Emily J., Capp, Michael W., Tsodikov, Oleg V., Record, M. Thomas

Journal:

Year:

2013

Language:

english

File:

PDF, 2.73 MB

english, 2013

35

Cover Picture: Chemical and Structural Insights into the Regioversatility of the Aminoglycoside Acetyltransferase Eis (ChemBioChem 16/2013)

Houghton, Jacob L., Biswas, Tapan, Chen, Wenjing, Tsodikov, Oleg V., Garneau-Tsodikova, Sylvie

Journal:

Year:

2013

Language:

english

File:

PDF, 596 KB

english, 2013

36

Structural Insight into MtmC, a Bifunctional Ketoreductase-Methyltransferase Involved in the Assembly of the Mithramycin Trisaccharide Chain

Chen, Jhong-Min, Hou, Caixia, Wang, Guojun, Tsodikov, Oleg V., Rohr, Jürgen

Journal:

Year:

2015

Language:

english

File:

PDF, 2.88 MB

english, 2015

37

Structure of inorganic pyrophosphatase from Staphylococcus aureus reveals conformational flexibility of the active site

Gajadeera, Chathurada S., Zhang, Xinyi, Wei, Yinan, Tsodikov, Oleg V.

Journal:

Journal of Structural Biology

Year:

2015

Language:

english

File:

PDF, 952 KB

english, 2015

38

Ambiguity of structure determination from a minimum of diffraction intensities

Al-Asadi, Ahmed, Leggas, Dimitri, Tsodikov, Oleg V.

Journal:

Acta Crystallographica Section A Foundations and Advances

Year:

2014

Language:

english

File:

PDF, 86 KB

english, 2014

39

Biochemical and Structural Analysis of an Eis Family Aminoglycoside Acetyltransferase from Bacillus anthracis

Green, Keith D., Biswas, Tapan, Chang, Changsoo, Wu, Ruiying, Chen, Wenjing, Janes, Brian K., Chalupska, Dominika, Gornicki, Piotr, Hanna, Philip C., Tsodikov, Oleg V., Joachimiak, Andrzej, Garneau-Ts

Journal:

Year:

2015

Language:

english

File:

PDF, 11.55 MB

english, 2015

40

New Insights into Fluoroquinolone Resistance in Mycobacterium tuberculosis: Functional Genetic Analysis of gyrA and gyrB Mutations

Malik, Seidu, Willby, Melisa, Sikes, David, Tsodikov, Oleg V., Posey, James E., Via, Laura Ellen

Journal:

Year:

2012

Language:

english

File:

PDF, 407 KB

english, 2012

41

Determination of small crystal structures from a minimum set of diffraction intensities by homotopy continuation

Leggas, Dimitri, Tsodikov, Oleg V.

Journal:

Acta Crystallographica Section A Foundations and Advances

Year:

2015

Language:

english

File:

PDF, 235 KB

english, 2015

42

Organized Unidirectional Waves of ATP Hydrolysis within a RecA Filament

Cox, Julia M., Tsodikov, Oleg V., Cox, Michael M.

Journal:

Year:

2005

Language:

english

File:

PDF, 32 KB

english, 2005

43

Structural and computational dissection of the catalytic mechanism of the inorganic pyrophosphatase from Mycobacterium tuberculosis

Pratt, Andrew C., Dewage, Sajeewa W., Pang, Allan H., Biswas, Tapan, Barnard-Britson, Sandra, Cisneros, G. Andrés, Tsodikov, Oleg V.

Journal:

Journal of Structural Biology

Year:

2015

Language:

english

File:

PDF, 2.41 MB

english, 2015

44

Unusual regioversatility of acetyltransferase Eis, a cause of drug resistance in XDR-TB

Wenjing Chen, Tapan Biswas, Vanessa R. Porter, Oleg V. Tsodikov and Sylvie Garneau-Tsodikova

Journal:

Proceedings of the National Academy of Sciences

Year:

2011

Language:

english

File:

PDF, 1.32 MB

english, 2011

45

Par-4 secretion: stoichiometry of 3-arylquinoline binding to vimentin

Sviripa, Vitaliy M., Burikhanov, Ravshan, Obiero, Josiah M., Yuan, Yaxia, Nickell, Justin R., Dwoskin, Linda P., Zhan, Chang-Guo, Liu, Chunming, Tsodikov, Oleg V., Rangnekar, Vivek M., Watt, David S.

Journal:

Organic & Biomolecular Chemistry

Year:

2016

Language:

english

File:

PDF, 670 KB

english, 2016

46

Structural basis for dimerization and DNA binding of transcription factor FLI1

Hou, Caixia, Tsodikov, Oleg V

Journal:

Year:

2015

Language:

english

File:

PDF, 3.86 MB

english, 2015

47

Crystal structure ofO-methyltransferase CalO6 from the calicheamicin biosynthetic pathway: a case of challenging structure determination at low resolution

Tsodikov, Oleg V., Hou, Caixia, Walsh, Christopher T., Garneau-Tsodikova, Sylvie

Journal:

BMC Structural Biology

Year:

2015

Language:

english

File:

PDF, 1.27 MB

english, 2015

48

Dimerization and DNA recognition rules of mithramycin and its analogues

Weidenbach, Stevi, Hou, Caixia, Chen, Jhong-Min, Tsodikov, Oleg V., Rohr, Jürgen

Journal:

Journal of Inorganic Biochemistry

Year:

2015

Language:

english

File:

PDF, 657 KB

english, 2015

49

Potent inhibitors of acetyltransferase Eis overcome kanamycin re-sistance in Mycobacterium tuberculosis

Willby, Melisa J., Green, Keith D., Gajadeera, Chathurada S., Hou, Caixia, Tsodikov, Oleg V, Posey, James E., Garneau-Tsodikova, Sylvie

Journal:

ACS Chemical Biology

Year:

2016

Language:

english

File:

PDF, 1.08 MB

english, 2016

50

Structures of mithramycin analogues bound to DNA and implications for targeting transcription factor FLI1

Hou, Caixia, Weidenbach, Stevi, Cano, Kristin E., Wang, Zhonghua, Mitra, Prithiba, Ivanov, Dmitri N., Rohr, Jürgen, Tsodikov, Oleg V.

Journal:

Nucleic Acids Research

Year:

2016

Language:

english

File:

PDF, 6.13 MB

english, 2016

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