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Free energy based populations of interconverting microstates of a cyclic peptide lead to the experimental NMR data.
Analysis of nuclear Overhauser enhancement (NOE) intensities data of interconverting microstates of a peptide is a difficult problem in nmr. A new statistical mechanics methodology has been proposed… Expand
DETERMINATION OF THE STABLE MICROSTATES OF A PEPTIDE FROM NOE DISTANCE CONSTRAINTS AND OPTIMIZATION OF ATOMIC SOLVATION PARAMETERS
A methodology for analyzing nuclear Overhauser effect (NOE) data of interconverting microstates of a peptide has been suggested recently, which is based on pure statistical mechanical considerations.… Expand
Ab initio prediction of the solution structures and populations of a cyclic pentapeptide in DMSO based on an implicit solvation model
Using a recently developed statistical mechanics methodology, the solution structures and populations of the cyclic pentapeptide cyclo(D‐Pro1–Ala2–Ala3–Ala4–Ala5) in DMSO are obtained ab initio,… Expand
Efficiency of the Local Torsional Deformations Method for Identifying the Stable Structures of Cyclic Molecules
A new method for generating the low-energy structures of a chain molecule was proposed recently by us. This is a stochastic process where at each step an energy-minimized structure is changed by… Expand
NOVEL PROCEDURE FOR DEVELOPING IMPLICIT SOLVATION MODELS FOR PEPTIDES AND PROTEINS
Solvation is an important factor in the structure stabilization of proteins. The free energy of solvation has been commonly approximated by summing the products of the atomic solvation parameters… Expand
New conformational search method based on local torsional deformations for cyclic molecules, loops in proteins, and dense polymer systems
We propose a conformational search method, based on local torsional deformations (LTD) for locating the low energy structures of cyclic peptides, loops in proteins or dense polymer systems. LTD is… Expand
Efficiency of simulated annealing for peptides with increasing geometrical restrictions
Simulated annealing (SA) is a popular global minimizer that can conveniently be applied to complex macromolecular systems. Thus, a molecular dynamics or a Monte Carlo simulation starts at high… Expand
Performance of efficient minimization algorithms as applied to models of peptides and proteins
We test the efficiency of three minimization algorithms as applied to models of peptides and proteins. These include: the limited memory quasi‐Newton (L‐BFGS) of Liu and Nocedal; the truncated Newton… Expand
On the transferability of atomic solvation parameters: Ab initio structural prediction of cyclic heptapeptides in DMSO.
A statistical mechanics methodology for predicting the solution structures and populations of peptides developed recently is based on a novel method for optimizing implicit solvation models, which… Expand
Contribution of Short-Range Intramolecular Interactions to Local Chain Dynamics
The effect of short-range intramolecular interactions on the probability distribution of conformational transitions between rotamers in polymers are examined by both numerical (Brownian dynamics… Expand