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Topological and energetic factors: what determines the structural details of the transition state ensemble and " on–route " intermediates for protein folding? An investigation for small globular proteins. Recent experimental results suggest that the native fold, or topology, plays a primary role in determining the structure of the transition state ensemble,(More)
We compare simulations using the generalized Born/surface area (GB/SA) implicit solvent model with simulations using explicit solvent (transferable intermolecular potential 3 point, TIP3P) to test the GB/SA algorithm. We use the replica exchange molecular dynamics method to sample the conformational phase space of two alpha-helical peptides, A21 and the Fs,(More)
We implement the replica exchange molecular dynamics algorithm to study the interactions of a model peptide (WALP-16) with an explicitly represented DPPC membrane bilayer. We observe the spontaneous, unbiased insertion of WALP-16 into the DPPC bilayer and its folding into an alpha-helix with a transbilayer orientation. The free energy surface suggests that(More)
A recent workshop titled "Quantitative Computational Biophysics" at Florida State University provided an overview of the state of the art in quantitative modeling of biomolecular systems. The presentations covered a wide range of interrelated topics, including the development and validation of force fields, the modeling of protein-protein interactions, the(More)
Experiments with fast folding proteins are beginning to address the relationship between collapse and folding. We investigate how different scenarios for folding can arise depending on whether the folding and collapse transitions are concurrent or whether a nonspecific collapse precedes folding. Many earlier studies have focused on the limit in which(More)
Molecular dynamics is a popular technique to simulate the behavior of physical systems, with resolution at the atomic scale. One of its limitations is that an enormous computational effort is required to simulate to realistic time spans. Conventional parallelization strategies have limited effectiveness in dealing with this difficulty. We recently(More)
We present a new approach to parallelization of important scientific applications. It is based on the observation that results of prior, related, simulations are often available. We use such data to parallelize the time domain. We demonstrate the effectiveness of our approach in Molecular Dynamics (MD) simulations, which are widely used in nano and nano-bio(More)
191 Background: For 10-15% of cancer patients, pain cannot be controlled using existing therapies (Zech et al., Pain, 63, 65-76, 1995). SP-SAP is the first targeted toxin to undergo phase I testing for pain. SP-SAP (Wiley and Lappi, Neurosci Lett, 230, 97-100, 1997) covalently linkes substance P (SP), a neuromodulator that binds to NK1 receptors on laminae(More)
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