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JCC
2008
88views more  JCC 2008»
13 years 8 months ago
A self-organizing algorithm for molecular alignment and pharmacophore development
Abstract: We present a method for simultaneous three-dimensional (3D) structure generation and pharmacophorebased alignment using a self-organizing algorithm called Stochastic Prox...
Deepak Bandyopadhyay, Dimitris K. Agrafiotis
JCC
2011
87views more  JCC 2011»
13 years 3 months ago
Determining equilibrium constants for dimerization reactions from molecular dynamics simulations
Abstract: With today’s available computer power, free energy calculations from equilibrium molecular dynamics simulations “via counting” become feasible for an increasing num...
Djurre H. De Jong, Lars V. Schäfer, Alex H. D...
JCC
2008
114views more  JCC 2008»
13 years 8 months ago
Molecular simulation of multistate peptide dynamics: A comparison between microsecond timescale sampling and multiple shorter tr
Abstract: Molecular dynamics simulations of the RN24 peptide, which includes a diverse set of structurally heterogeneous states, are carried out in explicit solvent. Two approaches...
Luca Monticelli, Eric J. Sorin, D. Peter Tieleman,...
INFOCOM
2012
IEEE
11 years 11 months ago
Data gathering in networks of bacteria colonies: Collective sensing and relaying using molecular communication
Abstract—The prospect of new biological and industrial applications that require communication in micro-scale, encourages research on the design of bio-compatible communication n...
Arash Einolghozati, Mohsen Sardari, Ahmad Beirami,...
JCC
2006
59views more  JCC 2006»
13 years 8 months ago
Comparison of implicit solvent models for the simulation of protein-surface interactions
Abstract: Empirical force field-based molecular simulations can provide valuable atomistic-level insights into protein
Yu Sun, Robert A. Latour