[Colloquium] REMINDER: 4/23 TTIC Colloquium: Bruce Donald, Duke University

Mon Apr 23 10:04:35 CDT 2018

 When:     Monday, April 23rd at *10:30 am*

Where:    TTIC, 6045 S Kenwood Avenue, 5th Floor, Room 526

Who:       Bruce Donald, Duke University

Title:  Some Mathematical and Computational Challenges Arising in
Structural Molecular Biology

Abstract: Computational protein design is a transformative field with
exciting prospects for advancing both basic science and translational
medical research. New algorithms blend discrete and continuous mathematics
to address the challenges of creating designer proteins. I will briefly
discuss recent progress in this area, including broadly-neutralizing
anti-HIV-1 antibodies that we have designed computationally and that are
now being tested in humans (clinical trial NCT03015181), as well as some
interesting open problems.

I will then address the related problem of reconstruction of biomolecular
dynamics from experimental observables, which requires the determination of
a conformational probability distribution. These distributions are not
fully constrained by the limited information from experiments, and thus the
problem has no unique solution. To resolve this ambiguity, the problem must
be regularized by making (hopefully reasonable) assumptions. I will present
new ways to both represent and visualize correlated inter-domain protein
motions.  We use Bingham distributions, based on a quaternion fit to
circular moments of a physics-based quadratic form. To find the optimal
solution for the distribution, we designed an efficient, provable
branch-and-bound algorithm that exploits the structure of analytical
solutions to the trigonometric moment problem. Hence, continuous
conformational PDFs can be determined directly from NMR measurements. The
representation works especially well for multi-domain systems with broad
conformational distributions.

Host: Mark Hallen <mhallen at ttic.edu>

For more information on the colloquium series or to subscribe to the
mailing list,please see http://www.ttic.edu/colloquium.php

Mary C. Marre
Administrative Assistant
*Toyota Technological Institute*
*6045 S. Kenwood Avenue*
*Room 504*
*Chicago, IL  60637*
*p:(773) 834-1757*
*f: (773) 357-6970*
*mmarre at ttic.edu <mmarre at ttic.edu>*

On Sun, Apr 22, 2018 at 5:48 PM, Mary Marre <mmarre at ttic.edu> wrote:

> When:     Monday, April 23rd at *10:30 am*
>
> Where:    TTIC, 6045 S Kenwood Avenue, 5th Floor, Room 526
>
> Who:       Bruce Donald, Duke University
>
>
> Title:  Some Mathematical and Computational Challenges Arising in
> Structural Molecular Biology
>
>
> Abstract: Computational protein design is a transformative field with
> exciting prospects for advancing both basic science and translational
> medical research. New algorithms blend discrete and continuous mathematics
> to address the challenges of creating designer proteins. I will briefly
> discuss recent progress in this area, including broadly-neutralizing
> anti-HIV-1 antibodies that we have designed computationally and that are
> now being tested in humans (clinical trial NCT03015181), as well as some
> interesting open problems.
>
> I will then address the related problem of reconstruction of biomolecular
> dynamics from experimental observables, which requires the determination of
> a conformational probability distribution. These distributions are not
> fully constrained by the limited information from experiments, and thus the
> problem has no unique solution. To resolve this ambiguity, the problem must
> be regularized by making (hopefully reasonable) assumptions. I will present
> new ways to both represent and visualize correlated inter-domain protein
> motions.  We use Bingham distributions, based on a quaternion fit to
> circular moments of a physics-based quadratic form. To find the optimal
> solution for the distribution, we designed an efficient, provable
> branch-and-bound algorithm that exploits the structure of analytical
> solutions to the trigonometric moment problem. Hence, continuous
> conformational PDFs can be determined directly from NMR measurements. The
> representation works especially well for multi-domain systems with broad
> conformational distributions.
>
>
>
> Host: Mark Hallen <mhallen at ttic.edu>
>
>
>
> For more information on the colloquium series or to subscribe to the
> mailing list,please see http://www.ttic.edu/colloquium.php
>
>
>
> Mary C. Marre
> Administrative Assistant
> *Toyota Technological Institute*
> *6045 S. Kenwood Avenue*
> *Room 504*
> *Chicago, IL  60637*
> *p:(773) 834-1757*
> *f: (773) 357-6970*
> *mmarre at ttic.edu <mmarre at ttic.edu>*
>
> On Mon, Apr 16, 2018 at 4:52 PM, Mary Marre <mmarre at ttic.edu> wrote:
>
>> When:     Monday, April 23rd at *10:30 am*
>>
>> Where:    TTIC, 6045 S Kenwood Avenue, 5th Floor, Room 526
>>
>> Who:       Bruce Donald, Duke University
>>
>>
>> Title:  Some Mathematical and Computational Challenges Arising in
>> Structural Molecular Biology
>>
>>
>> Abstract: Computational protein design is a transformative field with
>> exciting prospects for advancing both basic science and translational
>> medical research. New algorithms blend discrete and continuous mathematics
>> to address the challenges of creating designer proteins. I will briefly
>> discuss recent progress in this area, including broadly-neutralizing
>> anti-HIV-1 antibodies that we have designed computationally and that are
>> now being tested in humans (clinical trial NCT03015181), as well as some
>> interesting open problems.
>>
>> I will then address the related problem of reconstruction of biomolecular
>> dynamics from experimental observables, which requires the determination of
>> a conformational probability distribution. These distributions are not
>> fully constrained by the limited information from experiments, and thus the
>> problem has no unique solution. To resolve this ambiguity, the problem must
>> be regularized by making (hopefully reasonable) assumptions. I will present
>> new ways to both represent and visualize correlated inter-domain protein
>> motions.  We use Bingham distributions, based on a quaternion fit to
>> circular moments of a physics-based quadratic form. To find the optimal
>> solution for the distribution, we designed an efficient, provable
>> branch-and-bound algorithm that exploits the structure of analytical
>> solutions to the trigonometric moment problem. Hence, continuous
>> conformational PDFs can be determined directly from NMR measurements. The
>> representation works especially well for multi-domain systems with broad
>> conformational distributions.
>>
>>
>>
>> Host: Mark Hallen <mhallen at ttic.edu>
>>
>>
>>
>> For more information on the colloquium series or to subscribe to the
>> mailing list,please see http://www.ttic.edu/colloquium.php
>>
>>
>>
>> Mary C. Marre
>> Administrative Assistant
>> *Toyota Technological Institute*
>> *6045 S. Kenwood Avenue*
>> *Room 504*
>> *Chicago, IL  60637*
>> *p:(773) 834-1757*
>> *f: (773) 357-6970*
>> *mmarre at ttic.edu <mmarre at ttic.edu>*
>>
>
>
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