Proteopedia - User contributions [en]

User:John Karanicolas

2016-08-20T18:16:36Z

John Karanicolas:

Dr. John Karanicolas is currently an associate professor at the Fox Chase Cancer Center.

His primary goal is to develop structure-based approaches for modulating protein function using small-molecules. His lab explores two parallel paths towards this overarching goal: the first is re-engineering proteins so that a small-molecule can be used to “turn on” function, and the second is identifying small-molecules that naturally complement and occlude a protein surface to “turn off” function. They apply these tools to understand how specific protein interactions are responsible for normal and aberrant signal transduction in cells.

User:John Karanicolas

2014-11-24T20:26:09Z

John Karanicolas:

Dr. John Karanicolas is currently an associate professor in the Center for Computational Biology and the Department of Molecular Biosciences at the University of Kansas.

Dr. Karanicolas was granted a PhD from The Scripps Research Institute in 2003. He carried out his graduate studies in the laboratory of Professor Charles L. Brooks III, where he studied protein folding through analysis of molecular dynamics simulations. He has since completed a postdoctoral fellowship in the laboratory of Professor David Baker, at the University of Washington. Here, Dr. Karanicolas carried out theoretical and/or experimental aspects of several design projects, including altering the allosteric mechanism of integrin signal transduction and designing a peptide to inhibit tau fibril formation. His postdoctoral accomplishments culminated in his design of a de novo protein-protein interface from two proteins with no natural affinity for each other.

Dr. Karanicolas stresses his enthusiasm to apply protein design methodology as an effective means to deconstruct the complexity in a system of particular biomedical interest, cytokine signaling. Carefully designed molecules will reduce cytokine signaling to a series of single well-defined responses, allowing clear delineation of these complex pathways and leading to a new class of therapeutics.

User:John Karanicolas/Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations

2014-11-24T02:22:53Z

John Karanicolas: New page: Predicted distinct transient pocket containing structures for Bcl-2, Bcl-xL, and Mcl-1. These models were created using the pocket optimization process described in Johnson and Karanicola...

Predicted distinct transient pocket containing structures for Bcl-2, Bcl-xL, and Mcl-1.

These models were created using the pocket optimization process described in Johnson and Karanicolas (PLoS Computational Biology). Exemplars describing the pocket are included, as described in "Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations" Johnson and Karanicolas (in review). Further details are available in these works.

[[Image:Bcl2_1.pdb|Bcl-2_1]]
[[Image:Bcl2_2.pdb|Bcl-2_2]]
[[Image:Bcl2_3.pdb|Bcl-2_3]]
[[Image:Bclxl_1.pdb|Bcl-xL_1]]
[[Image:Bclxl_2.pdb|Bcl-xL_2]]
[[Image:Mcl1_1.pdb|Mcl-1_1]]
[[Image:Mcl1_2.pdb|Mcl-1_2]]
[[Image:Mcl1_3.pdb|Mcl-1_3]]

File:Mcl1 3.pdb

2014-11-24T02:11:18Z

John Karanicolas: Predicted distinct Mcl-1 structure 3 from "Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations" by Johnson and Karanicolas (in review).

== Summary ==
Predicted distinct Mcl-1 structure 3 from "Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations" by Johnson and Karanicolas (in review).
== Licensing ==
{{self|cc-by-sa-3.0}}

File:Mcl1 2.pdb

2014-11-24T02:10:47Z

John Karanicolas: Predicted distinct Mcl-1 structure 2 from "Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations" by Johnson and Karanicolas (in review).

== Summary ==
Predicted distinct Mcl-1 structure 2 from "Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations" by Johnson and Karanicolas (in review).
== Licensing ==
{{self|cc-by-sa-3.0}}

File:Mcl1 1.pdb

2014-11-24T02:10:02Z

John Karanicolas: Predicted distinct Mcl-1 structure 1 from "Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations" by Johnson and Karanicolas (in review).

== Summary ==
Predicted distinct Mcl-1 structure 1 from "Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations" by Johnson and Karanicolas (in review).
== Licensing ==
{{self|cc-by-sa-3.0}}

File:Bclxl 2.pdb

2014-11-24T02:09:24Z

John Karanicolas: Predicted distinct Bcl-xL structure 3 from "Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations" by Johnson and Karanicolas (in review).

== Summary ==
Predicted distinct Bcl-xL structure 3 from "Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations" by Johnson and Karanicolas (in review).
== Licensing ==
{{self|cc-by-sa-3.0}}

File:Bclxl 1.pdb

2014-11-24T02:08:44Z

John Karanicolas: Predicted distinct Bcl-xL structure 1 from "Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations" by Johnson and Karanicolas (in review).

== Summary ==
Predicted distinct Bcl-xL structure 1 from "Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations" by Johnson and Karanicolas (in review).
== Licensing ==
{{self|cc-by-sa-3.0}}

File:Bcl2 1.pdb

2014-11-24T02:08:15Z

John Karanicolas:

== Summary ==
Predicted distinct Bcl-2 structure 1 from "Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations" by Johnson and Karanicolas (in review).
== Licensing ==
{{self|cc-by-sa-3.0}}

File:Bcl2 2.pdb

2014-11-24T02:07:53Z

John Karanicolas:

== Summary ==
Predicted distinct Bcl-2 structure 2 from "Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations" by Johnson and Karanicolas (in review).
== Licensing ==
{{self|cc-by-sa-3.0}}

File:Bcl2 3.pdb

2014-11-24T02:07:17Z

John Karanicolas: Predicted distinct Bcl-2 structure 3 from "Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations" by Johnson and Karanicolas (in review).

== Summary ==
Predicted distinct Bcl-2 structure 3 from "Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations" by Johnson and Karanicolas (in review).
== Licensing ==
{{self|cc-by-sa-3.0}}

File:Bcl2 2.pdb

2014-11-24T02:06:42Z

John Karanicolas: Predicted distinct Bcl structure 2 from "Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations" by Johnson and Karanicolas (in review).

== Summary ==
Predicted distinct Bcl structure 2 from "Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations" by Johnson and Karanicolas (in review).
== Licensing ==
{{self|cc-by-sa-3.0}}

File:Bcl2 1.pdb

2014-11-24T02:04:22Z

John Karanicolas: Predicted distinct Bcl structure 1 from "Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations" by Johnson and Karanicolas (in review).

== Summary ==
Predicted distinct Bcl structure 1 from "Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations" by Johnson and Karanicolas (in review).
== Licensing ==
{{self|cc-by-sa-3.0}}

User:John Karanicolas/de novo protein binding pairs by computational design

2011-01-03T22:50:21Z

John Karanicolas:

Design models corresponding to de novo protein binding pairs

These design models were produced via the protocol described in Karanicolas et al (Molecular Cell, in press). Further details on the computational design protocol and the experimental characterization of these proteins are available in this published work.

[[Image:Design_0.pdb|Design #0]]
[[Image:Design_1.pdb|Design #1]]
[[Image:Design_2.pdb|Design #2]]
[[Image:Design_3.pdb|Design #3]]
[[Image:Design_4.pdb|Design #4]]
[[Image:Design_5.pdb|Design #5]]
[[Image:Design_6.pdb|Design #6]]
[[Image:Design_7.pdb|Design #7]]
[[Image:Design_8.pdb|Design #8]]
[[Image:Design_9.pdb|Design #9]]
[[Image:Design_10.pdb|Design #10]]
[[Image:Design_11.pdb|Design #11]]

User:John Karanicolas/de novo protein binding pairs by computational design

2011-01-03T22:48:01Z

John Karanicolas:

User:John Karanicolas/de novo protein binding pairs by computational design

2011-01-03T22:47:02Z

John Karanicolas:

Design models corresponding to de novo protein binding pairs

[[Design_0.pdb|Design #0]]

User:John Karanicolas/de novo protein binding pairs by computational design

2011-01-03T22:46:29Z

John Karanicolas:

Design models corresponding to de novo protein binding pairs

[[Image:Design_0.pdb|Design #0]]

User:John Karanicolas/de novo protein binding pairs by computational design

2011-01-03T22:39:56Z

John Karanicolas: New page: Design models corresponding to de novo protein binding pairs

Design models corresponding to de novo protein binding pairs

File:Design 11.pdb

2010-05-30T18:48:19Z

John Karanicolas: Design #11 from Karanicolas et al. (manuscript in preparation)

== Summary ==
Design #11 from Karanicolas et al. (manuscript in preparation)

== Licensing ==
{{self|cc-by-sa-3.0}}

File:Design 10.pdb

2010-05-30T18:47:45Z

John Karanicolas: Design #10 from Karanicolas et al. (manuscript in preparation)

== Summary ==
Design #10 from Karanicolas et al. (manuscript in preparation)

== Licensing ==
{{self|cc-by-sa-3.0}}

File:Design 9.pdb

2010-05-30T18:47:15Z

John Karanicolas: Design #9 from Karanicolas et al. (manuscript in preparation)

== Summary ==
Design #9 from Karanicolas et al. (manuscript in preparation)

== Licensing ==
{{self|cc-by-sa-3.0}}

File:Design 8.pdb

2010-05-30T18:46:47Z

John Karanicolas: Design #8 from Karanicolas et al. (manuscript in preparation)

== Summary ==
Design #8 from Karanicolas et al. (manuscript in preparation)

== Licensing ==
{{self|cc-by-sa-3.0}}

File:Design 7.pdb

2010-05-30T18:46:16Z

John Karanicolas: Design #7 from Karanicolas et al. (manuscript in preparation)

== Summary ==
Design #7 from Karanicolas et al. (manuscript in preparation)

== Licensing ==
{{self|cc-by-sa-3.0}}

File:Design 6.pdb

2010-05-30T18:45:43Z

John Karanicolas: Design #6 from Karanicolas et al. (manuscript in preparation)

== Summary ==
Design #6 from Karanicolas et al. (manuscript in preparation)

== Licensing ==
{{self|cc-by-sa-3.0}}

File:Design 5.pdb

2010-05-30T18:45:12Z

John Karanicolas: Design #5 from Karanicolas et al. (manuscript in preparation)

== Summary ==
Design #5 from Karanicolas et al. (manuscript in preparation)

== Licensing ==
{{self|cc-by-sa-3.0}}

File:Design 4.pdb

2010-05-30T18:44:38Z

John Karanicolas: Design #4 from Karanicolas et al. (manuscript in preparation)

== Summary ==
Design #4 from Karanicolas et al. (manuscript in preparation)

== Licensing ==
{{self|cc-by-sa-3.0}}

File:Design 3.pdb

2010-05-30T18:44:02Z

John Karanicolas: Design #3 from Karanicolas et al. (manuscript in preparation)

== Summary ==
Design #3 from Karanicolas et al. (manuscript in preparation)

== Licensing ==
{{self|cc-by-sa-3.0}}

File:Design 2.pdb

2010-05-30T18:43:33Z

John Karanicolas: Design #2 from Karanicolas et al. (manuscript in preparation)

== Summary ==
Design #2 from Karanicolas et al. (manuscript in preparation)

== Licensing ==
{{self|cc-by-sa-3.0}}

File:Design 0.pdb

2010-05-30T18:42:56Z

John Karanicolas: uploaded a new version of "Image:Design 0.pdb": Design #0 from Karanicolas et al. (manuscript in preparation)

== Summary ==
Design #0 from Karanicolas et al. (manuscript in preparation)

== Licensing ==
{{self|cc-by-sa-3.0}}

File:Design 1.pdb

2010-05-30T18:41:41Z

John Karanicolas: uploaded a new version of "Image:Design 1.pdb": Design #1 from Karanicolas et al. (manuscript in preparation)

== Summary ==
Design #1 from Karanicolas et al. (manuscript in preparation)

== Licensing ==
{{self|cc-by-sa-3.0}}

File:Design 1.pdb

2010-05-30T18:37:46Z

John Karanicolas: Design #1 from Karanicolas et al. (manuscript in preparation)

== Summary ==
Design #1 from Karanicolas et al. (manuscript in preparation)

== Licensing ==
{{self|cc-by-sa-3.0}}

File:Design 0.pdb

2010-05-30T18:36:25Z

John Karanicolas: Design #0 from Karanicolas et al. (manuscript in preparation)

== Summary ==
Design #0 from Karanicolas et al. (manuscript in preparation)

== Licensing ==
{{self|cc-by-sa-3.0}}