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1

Advances in protein structure prediction and design

Kuhlman, Brian, Bradley, Philip

Journal:

Nature Reviews Molecular Cell Biology

Year:

2019

Language:

english

File:

PDF, 4.61 MB

english, 2019

2

Networked experiments and modeling for producing collective identity in a group of human subjects using an iterative abduction framework

Cedeno-Mieles, Vanessa, Hu, Zhihao, Ren, Yihui, Deng, Xinwei, Adiga, Abhijin, Barrett, Christopher, Contractor, Noshir, Ekanayake, Saliya, Epstein, Joshua M., Goode, Brian J., Korkmaz, Gizem, Kuhlman,

Journal:

Social Network Analysis and Mining

Year:

2020

Language:

english

File:

PDF, 3.39 MB

english, 2020

3

Control of microtubule dynamics using an optogenetic microtubule plus end–F-actin cross-linker

Adikes, Rebecca C., Hallett, Ryan A., Saway, Brian F., Kuhlman, Brian, Slep, Kevin C.

Journal:

The Journal of Cell Biology

Year:

2017

Language:

english

File:

PDF, 3.27 MB

english, 2017

4

Supertertiary Structure of the MAGUK Core from PSD-95

Zhang, Jun, Lewis, Steven M., Kuhlman, Brian, Lee, Andrew L.

Journal:

Year:

2013

Language:

english

File:

PDF, 1.30 MB

english, 2013

5

Engineering an improved light-induced dimer (iLID) for controlling the localization and activity of signaling proteins

Guntas, Gurkan, Hallett, Ryan A., Zimmerman, Seth P., Williams, Tishan, Yumerefendi, Hayretin, Bear, James E., Kuhlman, Brian

Journal:

Proceedings of the National Academy of Sciences

Year:

2015

Language:

english

File:

PDF, 1.55 MB

english, 2015

6

Fab-based bispecific antibody formats with robust biophysical properties and biological activity

Wu, Xiufeng, Sereno, Arlene J, Huang, Flora, Lewis, Steven M, Lieu, Ricky L, Weldon, Caroline, Torres, Carina, Fine, Cody, Batt, Micheal A, Fitchett, Jonathan R, Glasebrook, Andrew L, Kuhlman, Brian,

Journal:

Year:

2015

Language:

english

File:

PDF, 1.38 MB

english, 2015

7

Tuning the Binding Affinities and Reversion Kinetics of a Light Inducible Dimer Allows Control of Transmembrane Protein Localization

Zimmerman, Seth Parker, Hallett, Ryan, Bourke, Ashley M, Bear, James E., Kennedy, Matthew J, Kuhlman, Brian

Journal:

Year:

2016

Language:

english

File:

PDF, 8.95 MB

english, 2016

8

Structural Insights into Thioether Bond Formation in the Biosynthesis of Sactipeptides.

Grove, Tyler L., Himes, Paul Michael, Hwang, Sungwon, Yumerefendi, Hayretin, Bonanno, Jeffrey B., Kuhlman, Brian, Almo, Steven C., Bowers, Albert A.

Journal:

Journal of the American Chemical Society

Year:

2017

Language:

english

File:

PDF, 6.00 MB

english, 2017

9

Cells lay their own tracks: optogenetic Cdc42 activation stimulates fibronectin deposition supporting directed migration

Zimmerman, Seth P., Asokan, Sreeja B., Kuhlman, Brian, Bear, James E.

Journal:

Journal of Cell Science

Year:

2017

Language:

english

File:

PDF, 3.19 MB

english, 2017

10

Evolution of a highly active and enantiospecific metalloenzyme from short peptides

Studer, Sabine, Hansen, Douglas A., Pianowski, Zbigniew L., Mittl, Peer R. E., Debon, Aaron, Guffy, Sharon L., Der, Bryan S., Kuhlman, Brian, Hilvert, Donald

Journal:

Year:

2018

Language:

english

File:

PDF, 569 KB

english, 2018

11

Optogenetic control of cofilin and αTAT in living cells using Z-lock

Stone, Orrin J., Pankow, Neha, Liu, Bei, Sharma, Ved P., Eddy, Robert J., Wang, Hui, Putz, Andrew T., Teets, Frank D., Kuhlman, Brian, Condeelis, John S., Hahn, Klaus M.

Journal:

Nature Chemical Biology

Year:

2019

Language:

english

File:

PDF, 8.52 MB

english, 2019

12

An optogenetic switch for the Set2 methyltransferase provides evidence for transcription-dependent and -independent dynamics of H3K36 methylation

Lerner, Andrew M., Hepperla, Austin J., Keele, Gregory R., Meriesh, Hashem A., Yumerefendi, Hayretin, Restrepo, David, Zimmerman, Seth, Bear, James E., Kuhlman, Brian, Davis, Ian J., Strahl, Brian D.

Journal:

Genome Research

Year:

2020

File:

PDF, 6.21 MB

2020

13

Maintaining solvent accessible surface area under rotamer substitution for protein design

Andrew Leaver-Fay, Glenn L. Butterfoss, Jack Snoeyink, Brian Kuhlman

Journal:

Journal of Computational Chemistry

Year:

2007

Language:

english

File:

PDF, 125 KB

english, 2007

14

Amide proton exchange measurements as a probe of the stability and dynamics of the n-terminal domain of the ribosomal protein L9: Comparison with the intact protein

Liliya Vugmeyster, Brian Kuhlman, Daniel P. Raleigh

Journal:

Protein Science

Year:

1998

Language:

english

File:

PDF, 1.33 MB

english, 1998

15

Global analysis of the thermal and chemical denaturation of the N-terminal domain of the ribosomal protein L9 in H2O and D2O. Determination of the thermodynamic parameters, ΔH°, ΔS°, and ΔC°p, and evaluation of solvent isotope effects

Brian Kuhlman, Daniel P. Raleigh

Journal:

Protein Science

Year:

1998

Language:

english

File:

PDF, 832 KB

english, 1998

16

An improved protein decoy set for testing energy functions for protein structure prediction

Jerry Tsai, Richard Bonneau, Alexandre V. Morozov, Brian Kuhlman, Carol A. Rohl, David Baker

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2003

Language:

english

File:

PDF, 377 KB

english, 2003

17

A “solvated rotamer” approach to modeling water-mediated hydrogen bonds at protein–protein interfaces

Lin Jiang, Brian Kuhlman, Tanja Kortemme, David Baker

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 723 KB

english, 2005

18

Protein design simulations suggest that side-chain conformational entropy is not a strong determinant of amino acid environmental preferences

Xiaozhen Hu, Brian Kuhlman

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 154 KB

english, 2006

19

Using quantum mechanics to improve estimates of amino acid side chain rotamer energies

P. Douglas Renfrew, Glenn L. Butterfoss, Brian Kuhlman

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 335 KB

english, 2008

20

Computational design of second-site suppressor mutations at protein–protein interfaces

Deanne W. Sammond, Ziad M. Eletr, Carrie Purbeck, Brian Kuhlman

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 530 KB

english, 2010

21

Computational protein design with explicit consideration of surface hydrophobic patches

Ron Jacak, Andrew Leaver-Fay, Brian Kuhlman

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2012

Language:

english

File:

PDF, 1.40 MB

english, 2012

22

10.1038/89638

Nauli, Sehat, Kuhlman, Brian, Baker, David

Journal:

Natural Structural Biology

Year:

2001

Language:

english

File:

PDF, 1.39 MB

english, 2001

23

A genetically encoded photoactivatable Rac controls the motility of living cells

Wu, Yi I., Frey, Daniel, Lungu, Oana I., Jaehrig, Angelika, Schlichting, Ilme, Kuhlman, Brian, Hahn, Klaus M.

Journal:

Year:

2009

Language:

english

File:

PDF, 947 KB

english, 2009

24

Hold me tightly LOV

Hahn, Klaus M, Kuhlman, Brian

Journal:

Year:

2010

Language:

english

File:

PDF, 408 KB

english, 2010

25

E2 conjugating enzymes must disengage from their E1 enzymes before E3-dependent ubiquitin and ubiquitin-like transfer

Eletr, Ziad M, Huang, Danny T, Duda, David M, Schulman, Brenda A, Kuhlman, Brian

Journal:

Nature Structural and Molecular Biology

Year:

2005

Language:

english

File:

PDF, 168 KB

english, 2005

26

Catalysis by a De Novo Zinc-Mediated Protein Interface: Implications for Natural Enzyme Evolution and Rational Enzyme Engineering

Der, Bryan S., Edwards, David R., Kuhlman, Brian

Journal:

Year:

2012

Language:

english

File:

PDF, 1.83 MB

english, 2012

27

Designing Photoswitchable Peptides Using the AsLOV2 Domain

Oana I. Lungu, Ryan A. Hallett, Eun Jung Choi, Mary J. Aiken, Klaus M. Hahn, Brian Kuhlman

Journal:

Chemistry & Biology

Year:

2012

Language:

english

File:

PDF, 1.16 MB

english, 2012

28

Exploring folding free energy landscapes using computational protein design

Brian Kuhlman, David Baker

Journal:

Current Opinion in Structural Biology

Year:

2004

Language:

english

File:

PDF, 282 KB

english, 2004

29

Design of protein conformational switches

Xavier I Ambroggio, Brian Kuhlman

Journal:

Current Opinion in Structural Biology

Year:

2006

Language:

english

File:

PDF, 212 KB

english, 2006

30

Engineering and Design

Brian Kuhlman, William F DeGrado

Journal:

Current Opinion in Structural Biology

Year:

2009

Language:

english

File:

PDF, 76 KB

english, 2009

31

Computational design of affinity and specificity at protein–protein interfaces

John Karanicolas, Brian Kuhlman

Journal:

Current Opinion in Structural Biology

Year:

2009

Language:

english

File:

PDF, 901 KB

english, 2009

32

A Conformational Transition State Accompanies Tryptophan Activation by B. stearothermophilus Tryptophanyl-tRNA Synthetase

Maryna Kapustina, Violetta Weinreb, Li Li, Brian Kuhlman, Charles W. Carter Jr.

Journal:

Year:

2007

Language:

english

File:

PDF, 2.22 MB

english, 2007

33

Computer-Based Redesign of a β Sandwich Protein Suggests that Extensive Negative Design Is Not Required for De Novo β Sheet Design

Xiaozhen Hu, Huanchen Wang, Hengming Ke, Brian Kuhlman

Journal:

Year:

2008

Language:

english

File:

PDF, 980 KB

english, 2008

34

Increasing Sequence Diversity with Flexible Backbone Protein Design: The Complete Redesign of a Protein Hydrophobic Core

Grant S. Murphy, Jeffrey L. Mills, Michael J. Miley, Mischa Machius, Thomas Szyperski, Brian Kuhlman

Journal:

Year:

2012

Language:

english

File:

PDF, 1.63 MB

english, 2012

35

Social and photoperiod effects on reproduction in five species of Peromyscus

Brian C. Trainor, Lynn B. Martin II, Kelly M. Greiwe, Joshua R. Kuhlman, Randy J. Nelson

Journal:

General and Comparative Endocrinology

Year:

2006

Language:

english

File:

PDF, 235 KB

english, 2006

36

Structural biology: Paper alert

Máire Convery, Caitrı́ona Dennis, Siân Rowsell, Brian Kuhlman, Tanja Kortemme, Viara Grantcharova, Alex Watters, Andreas Engel, J Bernard Heymann, Francisco Melo, Gary Parkinson, Rob Russell, Richard

Journal:

Current Opinion in Structural Biology

Year:

2000

Language:

english

File:

PDF, 74 KB

english, 2000

37

Structural biology: Paper alert

Máire Convery, Caitrı́ona Dennis, Siân Rowsell, Brian Kuhlman, Tanja Kortemme, Francisco Melo, Gary Parkinson, Rob Russell, Gianfranco Gilardi, Richard Newman, Irmgard Sinning, Sabine L Flitsch, Phili

Journal:

Current Opinion in Structural Biology

Year:

2000

Language:

english

File:

PDF, 162 KB

english, 2000

38

Structural biology: Paper alert

Máire Convery, Caitrı́ona Dennis, Siân Rowsell, Brian Kuhlman, Tanja Kortemme, Viara Grantcharova, Andreas Engel, Francisco Melo, Gary Parkinson, Rob Russell, Richard Newman, Sabine L Flitsch, Philip

Journal:

Current Opinion in Structural Biology

Year:

2000

Language:

english

File:

PDF, 69 KB

english, 2000

39

Structural biology

Máire Convery, Caitrı́ona Dennis, Siân Rowsell, Brian Kuhlman, Tanya Kortemme, Viara Grantcharova, Alex Watters, Andreas Engel, J.Bernard Heymann, Francisco Melo, Gary Parkinson, Rob Russell, Gianfran

Journal:

Current Opinion in Structural Biology

Year:

2000

Language:

english

File:

PDF, 98 KB

english, 2000

40

An exceptionally stable helix from the ribosomal protein L9: implications for protein folding and stability

Brian Kuhlman, Hui Yu Yang, Judith A. Boice, Robert Fairman, Daniel P. Raleigh

Journal:

Journal of Molecular Biology

Year:

1997

Language:

english

File:

PDF, 262 KB

english, 1997

41

Cooperative folding of a protein mini domain: the peripheral subunit-binding domain of the pyruvate dehydrogenase multienzyme complex

Shari Spector, Brian Kuhlman, Robert Fairman, Elsa Wong, Judith A Boice, Daniel P Raleigh

Journal:

Journal of Molecular Biology

Year:

1998

Language:

english

File:

PDF, 293 KB

english, 1998

42

Global analysis of the effects of temperature and denaturant on the folding and unfolding kinetics of the N-terminal domain of the protein L9

Brian Kuhlman, Donna L Luisi, Philip A Evans, Daniel P Raleigh

Journal:

Journal of Molecular Biology

Year:

1998

Language:

english

File:

PDF, 272 KB

english, 1998

43

Effects of varying the local propensity to form secondary structure on the stability and folding kinetics of a rapid folding mixed α/β protein: characterization of a truncation mutant of the N-terminal domain of the ribosomal protein L9

Donna L Luisi, Brian Kuhlman, Kostandinos Sideras, Philip A Evans, Daniel P Raleigh

Journal:

Journal of Molecular Biology

Year:

1999

Language:

english

File:

PDF, 217 KB

english, 1999

44

Accurate computer-based design of a new backbone conformation in the second turn of protein L

Brian Kuhlman, Jason W O’Neill, David E Kim, Kam Y.J Zhang, David Baker

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 281 KB

english, 2002

45

Rapid E2-E3 Assembly and Disassembly Enable Processive Ubiquitylation of Cullin-RING Ubiquitin Ligase Substrates

Gary Kleiger, Anjanabha Saha, Steven Lewis, Brian Kuhlman, Raymond J. Deshaies

Journal:

Year:

2009

Language:

english

File:

PDF, 1.56 MB

english, 2009

46

Mis-translation of a Computationally Designed Protein Yields an Exceptionally Stable Homodimer: Implications for Protein Engineering and Evolution

Gautam Dantas, Alexander L. Watters, Bradley M. Lunde, Ziad M. Eletr, Nancy G. Isern, Toby Roseman, Jan Lipfert, Sebastian Doniach, Martin Tompa, Brian Kuhlman, Barry L. Stoddard, Gabriele Varani, Dav

Journal:

Journal of Molecular Biology

Year:

2006

Language:

english

File:

PDF, 1.15 MB

english, 2006

47

High-resolution Structural and Thermodynamic Analysis of Extreme Stabilization of Human Procarboxypeptidase by Computational Protein Design

Gautam Dantas, Colin Corrent, Steve L. Reichow, James J. Havranek, Ziad M. Eletr, Nancy G. Isern, Brian Kuhlman, Gabriele Varani, Ethan A. Merritt, David Baker

Journal:

Journal of Molecular Biology

Year:

2007

Language:

english

File:

PDF, 1.71 MB

english, 2007

48

Sequence Determinants of E2-E6AP Binding Affinity and Specificity

Ziad M. Eletr, Brian Kuhlman

Journal:

Journal of Molecular Biology

Year:

2007

Language:

english

File:

PDF, 584 KB

english, 2007

49

Structure-based Protocol for Identifying Mutations that Enhance Protein–Protein Binding Affinities

Deanne W. Sammond, Ziad M. Eletr, Carrie Purbeck, Randall J. Kimple, David P. Siderovski, Brian Kuhlman

Journal:

Journal of Molecular Biology

Year:

2007

Language:

english

File:

PDF, 1.57 MB

english, 2007

50

Computational Design of a PAK1 Binding Protein

Ramesh K. Jha, Andrew Leaver-Fay, Shuangye Yin, Yibing Wu, Glenn L. Butterfoss, Thomas Szyperski, Nikolay V. Dokholyan, Brian Kuhlman

Journal:

Journal of Molecular Biology

Year:

2010

Language:

english

File:

PDF, 1.48 MB

english, 2010

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