Simulating protein folding with full atomistic detail / Vijay S. Pande.

Format:

Video

Author/Creator:

Pande, Vijay S., author.

Language:

English

Subjects (All):

Computer simulation.

Physical Description:

1 online resource (1 streaming video file (42 min., 02 sec.)) : sound, color

Place of Publication:

London, England : Henry Stewart Talks, 2007.

System Details:

video file

Contents:

Introduction Protein folding and disease Folding kinetics can have a biological impact Why physical simulation? Primary challenges: timescale vs. accuracy Range of possible models Atomistic models Building an atomistic model Short range interactions Charge-charge interactions How do we get parameters? Existing forcefields What about water? Hydrophobic effect Dielectric properties Implicit solvation model: PB/SA - PB Implicit solvation model: PB/SA - SA Solvation models How good are these models? Aren't molecular models flawed? Comparison with experiment Water model can have a big impact Are forcefields good enough? The problem of sampling Experimentally relevant timescales Folding@home: worldwide grid computing Traditional approach: parallelism Simulating two-state dynamics New method: build Markovian state model MSM - plan (1) MSM - plan (2) Kinetics: predicted vs. experiment Challenge of analysing the data The role of chemical detail in folding mechanism Problem: complex dynamics P-fold: ordering states along the folding reaction Is water configuration relevant? Do we need an explicit representation for water? Results Challenge of protein folding Protein folding theory Zinc finger fold: BBA6 General folding properties - independent of water Three helix bundle: villin headpiece MSM for villin: kinetics How do proteins fold? Acknowledgements.

Notes:

Description based on: online resource; title from PDF information screen (Henry Stewart Talks Biomedical and Life Sciences Collection, viewed April 13 2024).

Retrieved April 13, 2024, from https://hstalks.com/bs/436/.