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1

An optimized protocol for the multigram synthesis of 3-(trifluoromethyl)bicyclo[1.1.1]pent-1-ylglycine (CF3-Bpg)

Pavel K. Mykhailiuk, Nataliia M. Voievoda, Sergii Afonin, Anne S. Ulrich, Igor V. Komarov

Journal:

Journal of Fluorine Chemistry

Year:

2010

Language:

english

File:

PDF, 292 KB

english, 2010

2

Incorporation of labile trans-4,5-difluoromethanoproline into a peptide as a stable label for 19F NMR structure analysis

Kubyshkin, Vladimir S., Mykhailiuk, Pavel K., Afonin, Sergii, Grage, Stephan L., Komarov, Igor V., Ulrich, Anne S.

Journal:

Journal of Fluorine Chemistry

Year:

2013

Language:

english

File:

PDF, 1.16 MB

english, 2013

3

Cyanato- and thiocyanato-substituted triangular clusters of molybdenum, [Mo 3 S 4 (dppe) 3 X 3 ] + (X = NCO − , NCS − ; dppe = 1,2-bis(diphenylphosphino)ethane)

Afonin, Mikhail Yu., Smolentsev, Anton I., Konchenko, Sergey N., Petrov, Pavel A.

Journal:

Journal of Coordination Chemistry

Year:

2015

Language:

english

File:

PDF, 651 KB

english, 2015

4

A Convenient Route to Trifluoromethyl-Substituted Cyclopropane Derivatives

Mykhailiuk, Pavel, Afonin, Sergii, Ulrich, Anne, Komarov, Igor

Journal:

Year:

2008

Language:

english

File:

PDF, 100 KB

english, 2008

5

Structure Analysis and Conformational Transitions of the Cell Penetrating Peptide Transportan 10 in the Membrane-Bound State

Fanghänel, Susanne, Wadhwani, Parvesh, Strandberg, Erik, Verdurmen, Wouter P. R., Bürck, Jochen, Ehni, Sebastian, Mykhailiuk, Pavel K., Afonin, Sergii, Gerthsen, Dagmar, Komarov, Igor V., Brock, Rolan

Journal:

Year:

2014

Language:

english

File:

PDF, 3.10 MB

english, 2014

6

Q | R : quantum-based refinement

Zheng, Min, Reimers, Jeffrey R., Waller, Mark P., Afonine, Pavel V.

Journal:

Acta Crystallographica Section D Structural Biology

Year:

2017

Language:

english

File:

PDF, 1.01 MB

english, 2017

7

Conformationally Rigid Trifluoromethyl-Substituted α-Amino Acid Designed for Peptide Structure Analysis by Solid-State 19F NMR Spectroscopy

Pavel K. Mikhailiuk, Sergii Afonin, Alexander N. Chernega, Eduard B. Rusanov, Maxim O. Platonov, Galina G. Dubinina, Marina Berditsch, Anne S. Ulrich, Igor V. Komarov

Journal:

Angewandte Chemie

Year:

2006

Language:

english

File:

PDF, 108 KB

english, 2006

8

Synthesis of Trifluoromethyl-Substituted Proline Analogues as 19F NMR Labels for Peptides in the Polyproline II Conformation

Pavel K. Mykhailiuk, Sergii Afonin, Gennady V. Palamarchuk, Oleg V. Shishkin, Anne S. Ulrich, Igor V. Komarov

Journal:

Angewandte Chemie

Year:

2008

Language:

english

File:

PDF, 425 KB

english, 2008

9

Conformationally Rigid Trifluoromethyl-Substituted α-Amino Acid Designed for Peptide Structure Analysis by Solid-State 19F NMR Spectroscopy

Pavel K. Mikhailiuk, Sergii Afonin, Alexander N. Chernega, Eduard B. Rusanov, Maxim O. Platonov, Galina G. Dubinina, Marina Berditsch, Anne S. Ulrich, Igor V. Komarov

Journal:

Angewandte Chemie International Edition

Year:

2006

Language:

english

File:

PDF, 109 KB

english, 2006

10

Synthesis of Trifluoromethyl-Substituted Proline Analogues as 19F NMR Labels for Peptides in the Polyproline II Conformation

Pavel K. Mykhailiuk, Sergii Afonin, Gennady V. Palamarchuk, Oleg V. Shishkin, Anne S. Ulrich, Igor V. Komarov

Journal:

Angewandte Chemie International Edition

Year:

2008

Language:

english

File:

PDF, 425 KB

english, 2008

11

Evaluating the amino acid CF3-bicyclopentylglycine as a new label for solid-state 19F-NMR structure analysis of membrane-bound peptides

Sergii Afonin, Pavel K. Mikhailiuk, Igor V. Komarov, Anne S. Ulrich

Journal:

Journal of Peptide Science

Year:

2007

Language:

english

File:

PDF, 547 KB

english, 2007

12

Compatibility of the conformationally rigid CF3-Bpg side chain with the hydrophobic coiled-coil interface

Mario Salwiczek, Pavel K. Mikhailiuk, Sergii Afonin, Igor V. Komarov, Anne S. Ulrich, Beate Koksch

Journal:

Year:

2010

Language:

english

File:

PDF, 255 KB

english, 2010

13

Solid state 19F NMR parameters of fluorine-labeled amino acids. Part II: Aliphatic substituents

Stephan L. Grage, Ulrich H.N. Dürr, Sergii Afonin, Pavel K. Mikhailiuk, Igor V. Komarov, Anne S. Ulrich

Journal:

Journal of Magnetic Resonance

Year:

2008

Language:

english

File:

PDF, 323 KB

english, 2008

14

Coupling of receptor conformation and ligand orientation determine graded activity

Bruning, John B, Parent, Alexander A, Gil, German, Zhao, Min, Nowak, Jason, Pace, Margaret C, Smith, Carolyn L, Afonine, Pavel V, Adams, Paul D, Katzenellenbogen, John A

Journal:

Nature Chemical Biology

Year:

2010

Language:

english

File:

PDF, 1.55 MB

english, 2010

15

Crystal structure of an anti-interleukin-2 monoclonal antibody Fab complexed with an antigenic nonapeptide

Pavel V. Afonin, Andrey V. Fokin, Igor N. Tsygannik, Irina YU. Mikhailova, Lyudmila V. Onoprienko, Inna I. Mikhaleva, Vadim T. Ivanov, Tat'yana YU. Mareeva, Vladimir A. Nesmeyanov, Naiyin Li, Walter A

Journal:

Protein Science

Year:

2001

Language:

english

File:

PDF, 586 KB

english, 2001

16

phenix.mr_rosetta: molecular replacement and model rebuilding withPhenixandRosetta

Thomas C. Terwilliger, Frank DiMaio, Randy J. Read, David Baker, Gábor Bunkóczi, Paul D. Adams, Ralf W. Grosse-Kunstleve, Pavel V. Afonine, Nathaniel Echols

Journal:

Journal of Structural and Functional Genomics

Year:

2012

Language:

english

File:

PDF, 524 KB

english, 2012

17

Recent developments in phasing and structure refinement for macromolecular crystallography

Paul D Adams, Pavel V Afonine, Ralf W Grosse-Kunstleve, Randy J Read, Jane S Richardson, David C Richardson, Thomas C Terwilliger

Journal:

Current Opinion in Structural Biology

Year:

2009

Language:

english

File:

PDF, 198 KB

english, 2009

18

Incorporation of cis - and trans -4,5-Difluoromethanoprolines into Polypeptides

Kubyshkin, Vladimir S., Mykhailiuk, Pavel K., Afonin, Sergii, Ulrich, Anne S., Komarov, Igor V.

Journal:

Organic Letters

Year:

2012

Language:

english

File:

PDF, 472 KB

english, 2012

19

Neutron Diffraction Studies of a Class A β-Lactamase Toho-1 E166A/R274N/R276N Triple Mutant

Stephen J. Tomanicek, Matthew P. Blakeley, Jonathan Cooper, Yu Chen, Pavel V. Afonine, Leighton Coates

Journal:

Journal of Molecular Biology

Year:

2010

Language:

english

File:

PDF, 958 KB

english, 2010

20

The Phenix software for automated determination of macromolecular structures

Paul D. Adams, Pavel V. Afonine, Gábor Bunkóczi, Vincent B. Chen, Nathaniel Echols, Jeffrey J. Headd, Li-Wei Hung, Swati Jain, Gary J. Kapral, Ralf W. Grosse Kunstleve, Airlie J. McCoy, Nigel W. Moria

Journal:

Year:

2011

Language:

english

File:

PDF, 2.92 MB

english, 2011

21

A 19 F NMR Label to Substitute Polar Amino Acids in Peptides: A CF 3 -Substituted Analogue of Serine and Threonine

Tkachenko, Anton N., Mykhailiuk, Pavel K., Afonin, Sergii, Radchenko, Dmytro S., Kubyshkin, Vladimir S., Ulrich, Anne S., Komarov, Igor V.

Journal:

Angewandte Chemie

Year:

2013

Language:

english

File:

PDF, 480 KB

english, 2013

22

A 19 F NMR Label to Substitute Polar Amino Acids in Peptides: A CF 3 -Substituted Analogue of Serine and Threonine

Tkachenko, Anton N., Mykhailiuk, Pavel K., Afonin, Sergii, Radchenko, Dmytro S., Kubyshkin, Vladimir S., Ulrich, Anne S., Komarov, Igor V.

Journal:

Angewandte Chemie International Edition

Year:

2013

Language:

english

File:

PDF, 504 KB

english, 2013

23

The Alignment of Membrane-Active Peptides Depends on the Lipid Phase State as Viewed by solid state 19F-NMR

Afonin, Sergii, Grage, Stephan L., Ieronimo, Marco, Maisch, Daniel, Wadhwani, Parvesh, Mykhailiuk, Pavel K., Salgado, Jesus, Komarov, Igor V., Ulrich, Anne S.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 37 KB

english, 2009

24

Incorporation of cis - and trans -4,5-Difluoromethanoprolines into Polypeptides

Kubyshkin, Vladimir S., Mykhailiuk, Pavel K., Afonin, Sergii, Ulrich, Anne S., Komarov, Igor V.

Journal:

Organic Letters

Year:

2012

File:

PDF, 93 KB

2012

25

Design, Synthesis, and Application of a Trifluoromethylated Phenylalanine Analogue as a Label to Study Peptides by Solid-State 19 F NMR Spectroscopy

Tkachenko, Anton N., Radchenko, Dmytro S., Mykhailiuk, Pavel K., Afonin, Sergii, Ulrich, Anne S., Komarov, Igor V.

Journal:

Angewandte Chemie International Edition

Year:

2013

Language:

english

File:

PDF, 689 KB

english, 2013

26

Improved Crystallographic Structures Using Extensive Combinatorial Refinement

Nwachukwu, Jerome C., Southern, Mark R., Kiefer, James R., Afonine, Pavel V., Adams, Paul D., Terwilliger, Thomas C., Nettles, Kendall W.

Journal:

Year:

2013

Language:

english

File:

PDF, 2.23 MB

english, 2013

27

TLS from fundamentals to practice

Urzhumtsev, Alexandre, Afonine, Pavel V., Adams, Paul D.

Journal:

Crystallography Reviews

Year:

2013

Language:

english

File:

PDF, 802 KB

english, 2013

28

Inside Back Cover: Controlling Biological Activity with Light: Diarylethene-Containing Cyclic Peptidomimetics (Angew. Chem. Int. Ed. 13/2014)

Babii, Oleg, Afonin, Sergii, Berditsch, Marina, Reiβer, Sabine, Mykhailiuk, Pavel K., Kubyshkin, Vladimir S., Steinbrecher, Thomas, Ulrich, Anne S., Komarov, Igor V.

Journal:

Angewandte Chemie International Edition

Year:

2014

File:

PDF, 1.65 MB

2014

29

Controlling Biological Activity with Light: Diarylethene-Containing Cyclic Peptidomimetics

Babii, Oleg, Afonin, Sergii, Berditsch, Marina, Reiβer, Sabine, Mykhailiuk, Pavel K., Kubyshkin, Vladimir S., Steinbrecher, Thomas, Ulrich, Anne S., Komarov, Igor V.

Journal:

Angewandte Chemie International Edition

Year:

2014

Language:

english

File:

PDF, 797 KB

english, 2014

30

Controlling Biological Activity with Light: Diarylethene-Containing Cyclic Peptidomimetics

Babii, Oleg, Afonin, Sergii, Berditsch, Marina, Reiβer, Sabine, Mykhailiuk, Pavel K., Kubyshkin, Vladimir S., Steinbrecher, Thomas, Ulrich, Anne S., Komarov, Igor V.

Journal:

Angewandte Chemie

Year:

2014

Language:

english

File:

PDF, 790 KB

english, 2014

31

Innenrücktitelbild: Controlling Biological Activity with Light: Diarylethene-Containing Cyclic Peptidomimetics (Angew. Chem. 13/2014)

Babii, Oleg, Afonin, Sergii, Berditsch, Marina, Reiβer, Sabine, Mykhailiuk, Pavel K., Kubyshkin, Vladimir S., Steinbrecher, Thomas, Ulrich, Anne S., Komarov, Igor V.

Journal:

Angewandte Chemie

Year:

2014

File:

PDF, 1.67 MB

2014

32

CRYO-EM Atomic Model of Brome Mosaic Virus Derived from Direct Electron Detection Images and a Real-Space Model Optimization Protocol

Wang, Zhao, Hryc, Corey, Bammes, Benjamin, Afonine, Pavel, Jakana, Joanita, Chen, Dong-Hua, liu, xiangan, Baker, Matthew L., Kao, Cheng, Ludtke, Steve J., Schmid, Michael F., Adams, Paul, Chiu, Wah

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 48 KB

english, 2014

33

Switching the Antimicrobial Activity of Gramicidin S by Light

Babii, Oleg, Afonin, Segrii, Berditsch, Marina, Reisser, Sabine, Steinbrecher, Thomas, Mykhailiuk, Pavel, Komarov, Igor, Ulrich, Anne S.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 41 KB

english, 2014

34

Combining Crystallographic and Structure-Modeling Approaches in Macromolecular Crystallography

Terwilliger, Thomas C., DiMaio, Frank, Read, Randy J., Baker, David, Brunger, Axel T., Adams, Paul D., Afonine, Pavel V., Hung, Li-Wei

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 41 KB

english, 2014

35

Design and Synthesis of a Monofluoro-Substituted Aromatic Amino Acid as a Conformationally Restricted 19 F NMR Label for Membrane-Bound Peptides

Tkachenko, Anton N., Mykhailiuk, Pavel K., Radchenko, Dmytro S., Babii, Oleg, Afonin, Sergii, Ulrich, Anne S., Komarov, Igor V.

Journal:

European Journal of Organic Chemistry

Year:

2014

Language:

english

File:

PDF, 551 KB

english, 2014

36

Automated identification of elemental ions in macromolecular crystal structures

Echols, Nathaniel, Morshed, Nader, Afonine, Pavel V., McCoy, Airlie J., Miller, Mitchell D., Read, Randy J., Richardson, Jane S., Terwilliger, Thomas C., Adams, Paul D.

Journal:

Acta Crystallographica Section D Biological Crystallography

Year:

2014

Language:

english

File:

PDF, 1.52 MB

english, 2014

37

Stereochemical effects on the aggregation and biological properties of the fibril-forming peptide [KIGAKI]3 in membranes

Wadhwani, Parvesh, Reichert, Johannes, Strandberg, Erik, Bürck, Jochen, Misiewicz, Julia, Afonin, Sergii, Heidenreich, Nico, Fanghänel, Susanne, Mykhailiuk, Pavel K., Komarov, Igor V., Ulrich, Anne S.

Journal:

Physical Chemistry Chemical Physics

Year:

2013

Language:

english

File:

PDF, 1.97 MB

english, 2013

38

Design, Synthesis, and Application of a Trifluoromethylated Phenylalanine Analogue as a Label to Study Peptides by Solid-State 19 F NMR Spectroscopy

Tkachenko, Anton N., Radchenko, Dmytro S., Mykhailiuk, Pavel K., Afonin, Sergii, Ulrich, Anne S., Komarov, Igor V.

Journal:

Angewandte Chemie

Year:

2013

Language:

english

File:

PDF, 406 KB

english, 2013

39

γ-(S)-Trifluoromethyl proline: evaluation as a structural substitute of proline for solid state 19 F-NMR peptide studies

Kubyshkin, Vladimir, Afonin, Sergii, Kara, Sezgin, Budisa, Nediljko, Mykhailiuk, Pavel K., Ulrich, Anne S.

Journal:

Organic & Biomolecular Chemistry

Year:

2015

Language:

english

File:

PDF, 997 KB

english, 2015

40

On Strength Reserve Assessment for Prismatic Folded Plate Roof Structures

Kolchunov, Vitaly, Osovskih, Evgeny, Afonin, Pavel

Journal:

Applied Mechanics and Materials

Year:

2015

Language:

english

File:

PDF, 474 KB

english, 2015

41

Model morphing and sequence assignment after molecular replacement

Terwilliger, Thomas C., Read, Randy J., Adams, Paul D., Brunger, Axel T., Afonine, Pavel V., Hung, Li-Wei

Journal:

Acta Crystallographica Section D Biological Crystallography

Year:

2013

Language:

english

File:

PDF, 1.16 MB

english, 2013

42

Metrics for comparison of crystallographic maps

Urzhumtsev, Alexandre, Afonine, Pavel V., Lunin, Vladimir Y., Terwilliger, Thomas C., Adams, Paul D.

Journal:

Acta Crystallographica Section D Biological Crystallography

Year:

2014

Language:

english

File:

PDF, 1.59 MB

english, 2014

43

Evidence of Functional Protein Dynamics from X-Ray Crystallographic Ensembles

Kohn, Jonathan E., Afonine, Pavel V., Ruscio, Jory Z., Adams, Paul D., Head-Gordon, Teresa, Levitt, Michael

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 413 KB

english, 2010

44

The solvent component of macromolecular crystals

Weichenberger, Christian X., Afonine, Pavel V., Kantardjieff, Katherine, Rupp, Bernhard

Journal:

Acta Crystallographica Section D Biological Crystallography

Year:

2015

Language:

english

File:

PDF, 2.60 MB

english, 2015

45

FEM: feature-enhanced map

Afonine, Pavel V., Moriarty, Nigel W., Mustyakimov, Marat, Sobolev, Oleg V., Terwilliger, Thomas C., Turk, Dusan, Urzhumtsev, Alexandre, Adams, Paul D.

Journal:

Acta Crystallographica Section D Biological Crystallography

Year:

2015

Language:

english

File:

PDF, 10.07 MB

english, 2015

46

An atomic model of brome mosaic virus using direct electron detection and real-space optimization

Wang, Zhao, Hryc, Corey F., Bammes, Benjamin, Afonine, Pavel V., Jakana, Joanita, Chen, Dong-Hua, Liu, Xiangan, Baker, Matthew L., Kao, Cheng, Ludtke, Steven J., Schmid, Michael F., Adams, Paul D., Ch

Journal:

Nature Communications

Year:

2014

Language:

english

File:

PDF, 2.97 MB

english, 2014

47

Programming new geometry restraints: parallelity of atomic groups

Sobolev, Oleg V., Afonine, Pavel V., Adams, Paul D., Urzhumtsev, Alexandre

Journal:

Journal of Applied Crystallography

Year:

2015

Language:

english

File:

PDF, 480 KB

english, 2015

48

Visualizing chaperone-assisted protein folding

Horowitz, Scott, Salmon, Loïc, Koldewey, Philipp, Ahlstrom, Logan S, Martin, Raoul, Quan, Shu, Afonine, Pavel V, van den Bedem, Henry, Wang, Lili, Xu, Qingping, Trievel, Raymond C, Brooks, Charles L,

Journal:

Nature Structural and Molecular Biology

Year:

2016

Language:

english

File:

PDF, 2.18 MB

english, 2016

49

ChemInform Abstract: γ-(S)-Trifluoromethyl Proline: Evaluation as a Structural Substitute of Proline for Solid State 19 F-NMR Peptide Studies

Kubyshkin, Vladimir, Afonin, Sergii, Kara, Sezgin, Budisa, Nediljko, Mykhailiuk, Pavel K., Ulrich, Anne S.

Journal:

Year:

2015

File:

PDF, 17 KB

2015

50

One-pot regio- and stereoselective synthesis of tertiary phosphine chalcogenides with (E)-N-ethenyl-1,2-dihydroquinoline functionalities

Gusarova, Nina K., Volkov, Pavel A., Ivanova, Nina I., Khrapova, Kseniya O., Albanov, Alexander I., Afonin, Andrei V., Borodina, Tatyana N., Trofimov, Boris A.

Journal:

Tetrahedron Letters

Year:

2016

Language:

english

File:

PDF, 1.77 MB

english, 2016

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