Divisions 247th ACS National Meeting, Dallas, TX Abstract... http ...

247th ACS National Meeting, Dallas, TX Abstract...

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247th ACS National Meeting and Exposition March 16-20, 2014, Dallas, Texas Chemistry and Materials for Energy

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Divisions COMP

Emilio Esposito, Scott Wildman

Sunday, March 16, 2014

Oral Session Tracing Pathways in Biomolecular Simulation - AM Session Location:

Omni Dallas Hotel

Room:

Trinity 7

Cosponsored by:

BIOL, CINF, MEDI, PHYS

Organizers:

Ronald Levy, Chung Wong

Presiders:

Emilio Gallicchio

Duration:

8:30 am - 11:45 am Pres Time

Pub #

8:30 am

1

Presentation Title Folding@home: Simulating pathways in atomic detail on the seconds timescale, with applications to kinase conformational change and protein folding Vijay Pande

9:00 am

2

9:30 am

3

From protein folding to biomolecular machines of life Jose N Onuchic, Biman Jana. Equilibrium thermodynamics and folding kinetics of a short, fast-folding, beta-hairpin Camilo A Jimenez-Cruz, Angel E Garcia.

10:00 am

Intermission

10:15 am

4

10:45 am

5

11:15 am

6

How long does it take to equilibrate the unfolded state of a protein? Ronald M Levy, Nan-jie Deng, Wei Dai. Molecular and coarse-grained views of protein dynamics in the unfolded state Dmitrii E Makarov Simulating millisecond dynamics of RNA polymerase II translocation at atomic resolution using Markov State models Xuhui Huang

COMP


Sunday, March 16, 2014

Oral Session Tracing Pathways in Biomolecular Simulation - PM Session Location:

Omni Dallas Hotel

Room:

Trinity 7

Cosponsored by:


Organizers:


Presiders:

Chung Wong

Duration:

1:30 pm - 4:45 pm Pres Time

Pub #

1:30 pm

25

Presentation Title Long molecular dynamics simulations of proteins: Progress, promise, and problems David E. Shaw

1 of 3

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2:00 pm

26


Modeling the function and directionality of molecular motors and other challenging biological systems Arieh Warshel

2:30 pm

27

Enhanced sampling by accelerated molecular dynamics J. Andrew McCammon

3:00 pm 3:15 pm

Intermission 28

Application of the string method to map conformational transitions in large biomolecular systems Benoit Roux, Mikolai Fajer, Avisek Das, Yilin Meng.

3:45 pm

29

Phosphate release coupled to rotary motion of F1-ATPase Kei-ichi Okazaki, Gerhard Hummer.

4:15 pm

30

Atomistic and coarse-grained simulations of the self-assembly of the tau peptide Joan-Emma Shea

COMP


Monday, March 17, 2014


Omni Dallas Hotel

Room:

Trinity 7

Cosponsored by:


Organizers:


Presiders:

Chung Wong

Duration:


Pub #

8:30 am

52

Weighted ensemble simulation methodology: Progress and challenges Daniel M Zuckerman

Presentation Title

9:00 am

53

Atomistic simulation of protein-peptide binding with rigorous kinetics

9:30 am

54

Lillian Chong

10:00 am

Learning about transitions: Adaptive controls for the molecular dynamics database Thomas B Woolf, Yanif Ahmad, Sarana nutanong, I-Jeng Wang. Intermission

10:15 am

55

10:45 am

56

11:15 am

57

Determining reaction paths from milestoning calculations Ron Elber Orthogonal space sampling methods to enable quantitative free energy simulations Wei Yang Conformational and alchemical pathways in extended ensemble binding free energy calculations Emilio Gallicchio, Peng He, Lauren Wickstrom, Nanjie Deng, Ronald M Levy.

COMP


Monday, March 17, 2014

Oral Session Tracing Pathways in Biomolecular Simulation - PM Session

2 of 3

Location:

Omni Dallas Hotel

Room:

Trinity 7

Cosponsored by:


Organizers:

Chung Wong, Ronald Levy

Presiders:

Lillian Chong

Duration:

1:30 pm - 4:45 pm

14/03/2017 13:41


Pres Time

Pub #

1:30 pm

75

2:00 pm

76

2:30 pm

77


Presentation Title Understanding the role of acid in cellular processes with molecular simulations Charles L. Brooks III Calculation of ion permeation through biological ion channels via course-grained models employing atomic level input Rob D. Coalson Markov State Models of ATP movement across the mitochondrial membrane Michael Grabe

3:00 pm 3:15 pm

Intermission 78

Induced fit effects and water structure in modeling ligand binding to proteins: Conformational sampling, free energy perturbation molecular dynamics simulations, and kinetics of binding Richard A Friesner

3:45 pm

79

4:15 pm

80

Analysis of energy landscapes governing protein-protein association Sandor Vajda, Dima Kozakov, Dmitri Beglov, Ioannis Ch Paschalidis, Pirooz Vakili. Protein-protein interactions in the activity of inhibitor of κB kinase-β Michael R Jones, Angela K Wilson.

COMP


Tuesday, March 18, 2014


Omni Dallas Hotel

Room:

Trinity 7

Cosponsored by:


Organizers:


Presiders:

Chung Wong

Duration:


Pub #

8:30 am

102

9:00 am

103

Presentation Title Molecular simulations of MAb-MAb association Mauro Lapelosa, Tom Patapoff, Dan Zarraga. Electrostatic channeling of dihydrofolate in the dihydrofolate reductase/thymidylate synthase complex Peter M Kekenes-Huskey, Changsun Eun, Vince T Metzger, James A McCammon.

9:30 am

104

High-level QM/MM free energy calculations at affordable computational cost Gerhard Koenig, Phillip Hudson, Stefan Boresch, Henry L Woodcock.

10:00 am 10:15 am

Intermission 105

Molecular dynamics simulations of the activated cannabinoid CB2 receptor in complex with the inhibitory Gαi1β1γ2 protein Jagjeet Singh, Diane Lynch, Alan Grossfield, Nicholas Leioatts, Michael Pitman, Patricia Reggio.

10:45 am

106

Binding mode analysis of Sterol 24-C methyltransferase by docking and molecular dynamics simulation Asma Abro, Syed Sikander Azam.

11:15 am

3 of 3

107

WITHDRAWN

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