“Topohydrophobic positions” as key markers of globular protein folds Anne PouponJean-Paul Mornon Regular article Pages: 2 - 8
How possible is the detection of correlated mutations? P. TufféryM. DurandP. Darlu Regular article Pages: 9 - 15
Prediction of protein structure using a knowledge-based off-lattice united-residue force field and global optimization methods Adam LiwoJarosław PillardyHarold A. Scheraga Regular article Pages: 16 - 20
Neural networks to study invariant features of protein folding M. CompianiP. FariselliR. Casadio Regular article Pages: 21 - 26
Stabilization centers in various proteins Zsuzsanna DosztányiIstván Simon Regular article Pages: 27 - 32
Analyzing patterns between regular secondary structures using short structural building blocks defined by a hidden Markov model A. C. CamprouxP. TufferyS. Hazout Regular article Pages: 33 - 40
A statistical analytical approach to predict the secondary structure of proteins from amino acid sequence information Shrish TiwariBoojala V. B. Reddy Regular article Pages: 41 - 45
Prediction of stability changes upon single-site mutations using database-derived potentials Dimitri GilisMarianne Rooman Regular article Pages: 46 - 50
Molecular modeling of the hypoxia-inducible factor-1 (HIF-1) G. MichelE. MinetC. Michiels Regular article Pages: 51 - 56
SeqFold – fully automated fold recognition and modeling software – evaluation and application Krzysztof A. OlszewskiLisa YanDavid J. Edwards Regular article Pages: 57 - 61
Adaptive umbrella sampling of the potential energy: modified updating procedure of the umbrella potential and application to peptide folding Christian BartelsMichael SchaeferMartin Karplus Regular article Pages: 62 - 66
Dimer models for ErbB-2/neu transmembrane domains from molecular dynamics simulations Nicolas SajotNorbert GarnierMonique Genest Regular article Pages: 67 - 72
A new “hydrophobic template” method detects segments forming transmembrane α-helical bundles in ion channels Roman G. EfremovGérard VergotenAlexander S. Arseniev Regular article Pages: 73 - 76
Sequence classification of water channels and related proteins in view of functional predictions B. TallurJ. NicolasC. Delamarche Regular article Pages: 77 - 81
Molecular dynamics simulations of the isolated domain 1 of annexin I Tru HuynhGabriel MusatAlain Sanson Regular article Pages: 82 - 86
Dynamics of the transmembrane domain of the ErbB-2 receptor Jean-Pierre DuneauSerge CrouzyMonique Genest Regular article Pages: 87 - 91
Molecular modelling of amphipathic basic model peptides: Interactions in aqueous solutions and in the presence of lipids Denise SyCécile MangavelJean Antoine Reynaud Regular article Pages: 92 - 96
Ion channels of biological membranes: prediction of single channel conductance Kishani M. RanatungaCharlotte AdcockMark S. P. Sansom Regular article Pages: 97 - 102
C–H...O and C–H...N interactions in RNA structures Maria BrandlKlaus LindauerJürgen Sühnel Regular article Pages: 103 - 113
Sequence dependence of DNA radioprotection by the thiols WR-1065 and WR-151326 D. SyC. DurandM. Spotheim-Maurizot Regular article Pages: 114 - 120
Molecular modeling study of an abasic DNA undecamer duplex: d(GCGTGOGTGCG) · d(CGCACTCACGC) L. AyadiC. Coulombeau Regular article Pages: 121 - 125
Study of flexible joints and permanent bends in DNA fragments by brownian dynamics simulations Giuseppe ChiricoMaddalena Collini Regular article Pages: 126 - 130
MCSS-based predictions of RNA binding sites Fabrice LeclercMartin Karplus Regular article Pages: 131 - 137
Examining ligand-protein interactions with binding-energy landscapes Paul A. RejtoDjamal BouzidaGennady M. Verkhivker Regular article Pages: 138 - 142
Theoretical investigation of histidine-tryptophan preferential interactions Giuliano AlagonaCaterina GhioSusanna Monti Regular article Pages: 143 - 150
Theoretical pKa calculations of proteins; the tyrosine and lysine residues of b-elicitin Hans J. VogelAndré H. Juffer Regular article Pages: 159 - 162
Poisson-Boltzmann calculations versus molecular dynamics simulations for calculating the electrostatic potential of a solvated peptide Gerald Löffler Regular article Pages: 163 - 169
Peptides in membranes: assessment of environmental effects via simulations using an implicit solvation model Roman G. EfremovDmitry E. NoldeAlexander S. Arseniev Regular article Pages: 170 - 174
Identifying key electrostatic interactions in Rhizomucor miehei lipase: the influence of solvent dielectric Sanna JääskeläinenChandra S. VermaLeo S. D. Caves Regular article Pages: 175 - 179
The effect of the protein environment on the structure and charge distribution of the retinal Schiff base in bacteriorhodopsin Emadeddin TajkhorshidSándor Suhai Regular article Pages: 180 - 185
Prediction of solvent accessibility of amino acid residues: critical aspects M. H. Mucchielli-GiorgiP. TufféryS. Hazout Regular article Pages: 186 - 193
Solution conformations of structured peptides: continuum electrostatics versus distance-dependent dielectric functions Michael SchaeferChristian BartelsMartin Karplus Regular article Pages: 194 - 204
Enhanced protein crystallization around the metastable critical point Pieter Rein ten WoldeDaan Frenkel Regular article Pages: 205 - 208
Why betaine crystallizes in high local Cs symmetry. An ab initio MO and DFT study of anhydrous betaine and betaine monohydrate Tommi H. NyrönenReijo SuontamoIlkka Pitkänen Regular article Pages: 209 - 214
Structure effects on isomerization pathways and vibrational spectra of epoxysaccharides: a numerical study Svetlana G. KirillovaVictor M. AndrianovRostislav G. Zhbankov Regular article Pages: 215 - 222
Information about the biologically relevant properties of Clostridium pasteurianum rubredoxin obtained from modeling and dynamics simulations of molecular variants J.-M. Moulis Regular article Pages: 223 - 227
Transition state structure invariance to model system size and calculation levels: a QM/MM study of the carboxylation step catalyzed by Rubisco V. MolinerJ. AndrésO. Tapia Regular article Pages: 228 - 233
Transition-state structures for describing the enzyme-catalyzed mechanisms of rubisco J. AndrésM. OlivaO. Tapia Regular article Pages: 234 - 240
Modelling the active site of glyceraldehyde-3 phosphate dehydrogenase with the LSCF formalism Alain CartierDavid BrownGuy Branlant Regular article Pages: 241 - 245
