How accurate can molecular dynamics/linear response and Poisson–Boltzmann/solvent accessible surface calculations be for predicting relative binding affinities? Acetylcholinesterase huprine inhibitors as a test case X. BarrilJ. L. GelpíF. J. Luque Regular article Pages: 2 - 9
Influence of ligand binding on the conformation of Torpedo californica acetylcholinesterase Nathalie BoutonnetDaniel Van BelleShoshana J. Wodak Regular article Pages: 10 - 21
Prediction of DNA far-IR absorption spectra based on normal mode analysis Maria BykhovskaiaBoris GelmontKrystyna Zakrzewska Regular article Pages: 22 - 27
Exploring the use of a structural alphabet for structural prediction of protein loops A. C. CamprouxA. G. BrevernP. Tufféry Regular article Pages: 28 - 35
Compacting local protein folds with a “hybrid protein model” A. G. de BrevernS. Hazout Pages: 36 - 47
Implicit two-phase solvation model as a tool to assess conformation and energetics of proteins in membrane-mimetic media Roman EfremovPavel VolynskyAlexander Arseniev Regular article Pages: 48 - 54
Assessment of conformation and energetics of the N-terminal part of elafin via computer simulations Roman G. EfremovPavel E. VolynskyAlain J. P. Alix Regular article Pages: 55 - 61
Coupling overall rotations with modal dynamics J. ElezgarayG. MarcouY. H. Sanejouand Regular article Pages: 62 - 68
Ab initio structure predictions using a hierarchical approach applied to 434 cro and the Drosophila homeodomain Dimitri GilisMarianne Rooman Regular article Pages: 69 - 75
Extracting parameters for base-pair level models of DNA from molecular dynamics simulations Oscar GonzalezJohn H. Maddocks Regular article Pages: 76 - 82
Protein-induced DNA bending: the role of phosphate neutralisation Raphael GurlieKrystyna Zakrzewska Regular article Pages: 83 - 90
FIRE: predicting the spatial proximity of protein residues from 3D NOESY–HSQC T. E. MalliavinP. BartheM. A. Delsuc Regular article Pages: 91 - 97
A computational model of the 5-HT3 receptor extracellular domain: search for ligand binding sites Maria Cristina MenzianiFrancesca De RienzoPier G. De Benedetti Regular article Pages: 98 - 104
Quantum mechanical/molecular mechanical methods and the study of kinetic isotope effects: modelling the covalent junction region and application to the enzyme xylose isomerase R. Mark NicollSally A. HindleNeil A. Burton Regular article Pages: 105 - 112
Deciphering globular protein sequence–structure relationships: from observation to prediction A. PouponJ.-P. Mornon Regular article Pages: 113 - 120
Stabilization centers and protein stability Á. SimonZ. DosztányiI. Simon Regular article Pages: 121 - 127
Analysis of the RGD sequence in protein structures: comparison to the conformations of the RGDW and DRGDW peptides determined by molecular dynamics simulations Roland H. Stote Regular article Pages: 128 - 136
Modelling radiation-induced damage in the lac operator –lac repressor complex. DNA damage: 8-oxoguanine D. SyC. FlouzatM. Spotheim-Maurizot Regular article Pages: 137 - 145
Quantum mechanical/molecular mechanical study of three stationary points along the deacylation step of the catalytic mechanism of elastase Maya TopfPéter VárnaiW. Graham Richards Regular article Pages: 146 - 151
Theoretical studies of electron and hydrogen transfer reactions between semiquinone radicals and oxygen Yan-Ni WangLeif A. Eriksson Special article Pages: 158 - 162
