The German EMBnet node and genomic databases

Guest Scientists Dr. Salim Abdali (Lyngby, Denmark, 5 6/01) Dr. Yuriko Aoki (Hiroshima, Japan, 8 9/01; 8 9/02) Dr. István Andrejkovics (Debrecen, Hungary, 12/01-11/02) Attila Bende (Debrecen, Hungary, 10 12/01) Enikö Bende (Debrecen, Hungary, 12/01 11/02) Dr. István Csonka (Budapest, Hungary, 10/00 9/01) Anna Gaitova (Novosibirsk, Russia, 1/01 4/02) Alexander Garcia (Bogotá, Columbia, 08 9/01) Dr. Gábor Halász (Debrecen, Hungary, 7 8/01; 12/02 ) Prof. Akira Imamura (Hiroshima, Japan, 8/02) Dr. Karl Jalkanen (Lyngby, Denmark, 12/01 2/02) Zsuzsa Janosfalvi (Debrecen, Hungary, 1 4/02) Sunitha Jonnakuty (Hyderabad, India, 7/02 ) Dr. Ponmalalgounder Kolandaivel (Coimbatore, Indien, 07/ 01 09/01) Dr. Oleg Shishkin (Kharkov, Ukraine, 6 7/01) Pawel Siedlecki (Warsaw, Poland, 6 7/02; 10 12/02) Ferenc Tasnádi (Debrecen, Hungary, 10 12/01) Dr. Ágnes Vibók (Debrecen, Hungary, 7 8/01; 9/02 ) Dr. Hong-Yi Zhou (Beijing, China, 1 2/01).

[1]  Otto Ritter,et al.  A Feature-Based Approach to Discrimination and Prediction of Protein Folding , 2002 .

[2]  S. Suhai,et al.  Proton mobility in protonated glycylglycine and N-formylglycylglycinamide: a combined quantum chemical and RKKM study. , 2001, Rapid communications in mass spectrometry : RCM.

[3]  Jon Baker,et al.  Geometry optimization of large biomolecules in redundant internal coordinates , 2000 .

[4]  M. Elstner,et al.  Tetragonal crystalline carbon nitrides: theoretical predictions. , 2001, Physical review letters.

[5]  S Suhai,et al.  QM/MM study of the active site of free papain and of the NMA-papain complex. , 1999, Journal of biomolecular structure & dynamics.

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[13]  Sándor Suhai,et al.  The effect of the protein environment on the structure and charge distribution of the retinal Schiff base in bacteriorhodopsin , 1999 .

[14]  S. Suhai,et al.  Proton mobility and main fragmentation pathways of protonated lysylglycine. , 2001, Rapid communications in mass spectrometry : RCM.

[15]  Sándor Suhai,et al.  A Self‐Consistent Charge Density‐Functional Based Tight‐Binding Method for Predictive Materials Simulations in Physics, Chemistry and Biology , 2000 .

[16]  S. Suhai,et al.  Response of C60 and Cn to ultrashort laser pulses , 2001 .

[17]  S Suhai,et al.  Estimating linkage disequilibrium between a polymorphic marker locus and a trait locus in natural populations. , 1999, Genetics.

[18]  Sándor Suhai,et al.  Automatic Assembly and Editing of Genomic Data , 2002 .

[19]  Rebecca C. Wade,et al.  L-Alanyl-L-alanine in the zwitterionic state: structures determined in the presence of explicit water molecules and with continuum models using density functional theory , 1999 .

[20]  Sándor Suhai,et al.  Role of Isomerization Barriers in the pKa Control of the Retinal Schiff Base: A Density Functional Study , 1999 .

[21]  Sándor Suhai,et al.  Dielectric effects due to the environment on the structure and proton affinity of retinal Schiff base models , 1999 .

[22]  A. Carlo,et al.  Electronic band structure and intermolecular interaction in substituted thiophene polymorphs , 2001 .

[23]  Martin Senger,et al.  Distributed Application Management in Bioinformatics , 2002 .

[24]  Thomas Frauenheim,et al.  Atomistic simulations of complex materials: ground-state and excited-state properties , 2002 .

[25]  S Suhai,et al.  Formation of a2+ ions of protonated peptides. An ab initio study. , 2000, Rapid communications in mass spectrometry : RCM.

[26]  S. Suhai,et al.  Theoretical investigation of carbon defects and diffusion in α-quartz , 2001 .

[27]  K Schulten,et al.  Molecular dynamics study of the nature and origin of retinal's twisted structure in bacteriorhodopsin. , 2000, Biophysical journal.

[28]  Sándor Suhai,et al.  A comparative study of MP2, B3LYP, RHF and SCC-DFTB force fields in predicting the vibrational spectra of N-acetyl-L-alanine-N'-methyl amide: VA and VCD spectra , 1999 .

[29]  S. Suhai,et al.  Combined quantum chemical and RRKM modeling of the main fragmentation pathways of protonated GGG. I. Cis‐trans isomerization around protonated amide bonds , 2001 .

[30]  M Elstner,et al.  Quantum mechanics simulation of protein dynamics on long timescale , 2001, Proteins.

[31]  Sándor Suhai,et al.  The dielectric effect of the environment on the p K a of the retinal Schiff base and on the stabilization of the ion pair in bacteriorhodopsin , 2000 .

[32]  Martin Reczko,et al.  Protein Fold Class Prediction: New Methods of Statistical Classification , 1999, ISMB.

[33]  Pavel Hobza,et al.  Reliable theoretical treatment of molecular clusters: Counterpoise-corrected potential energy surface and anharmonic vibrational frequencies of the water dimer , 1999 .

[34]  E. Tajkhorshid,et al.  Performance of the AM1, PM3, and SCC-DFTB methods in the study of conjugated Schiff base molecules , 2002 .

[35]  Sándor Suhai,et al.  Influence of the Methyl Groups on the Structure, Charge Distribution, and Proton Affinity of the Retinal Schiff Base , 1999 .

[36]  Sándor Suhai,et al.  Structures, vibrational absorption and vibrational circular dichroism spectra of L-alanine in aqueous solution: a density functional theory and RHF study , 2000 .

[37]  Peter Pulay,et al.  Newtonian molecular dynamics in general curvilinear internal coordinates , 2002 .

[38]  Sándor Suhai,et al.  Electronic effects on the ground-state rotational barrier of polyene Schiff bases: A molecular orbital study , 1999 .

[39]  Sándor Suhai,et al.  Intermolecular bond lengths: extrapolation to the basis set limit on uncorrected and BSSE-corrected potential energy hypersurfaces , 2001, J. Comput. Chem..

[40]  Sándor Suhai,et al.  On the effect of the BSSE on intermolecular potential energy surfaces. Comparison of a priori and a posteriori BSSE correction schemes , 2001, J. Comput. Chem..

[41]  Sándor Suhai,et al.  Towards understanding some ion intensity relationships for the tandem mass spectra of protonated peptides. , 2002, Rapid communications in mass spectrometry : RCM.

[42]  Thomas Frauenheim,et al.  Hydrogen bonding and stacking interactions of nucleic acid base pairs: A density-functional-theory based treatment , 2001 .

[43]  S. Suhai,et al.  Application of an approximate density-functional method to sulfur containing compounds , 2001 .

[44]  K. Frimand,et al.  SCC-TB, DFT/B3LYP, MP2, AM1, PM3 and RHF study of ethylene oxide and propylene oxide structures, VA and VCD spectra , 2002 .

[45]  Thomas Frauenheim,et al.  Hybrid SCC-DFTB/molecular mechanical studies of H-bonded systems and ofN-acetyl-(L-Ala)nN?-methylamide helices in water solution , 2000 .

[46]  S. Suhai,et al.  Theoretical determination of the vibrational absorption and Raman spectra of 3-methylindole and 3-methylindole radicals , 2001 .

[47]  M. Knapp-Mohammady,et al.  Proteine: Struktur, Dynamik, Funktion , 1999 .

[48]  Sandor Suhai.  Genomics and Proteomics: Functional and Computational Aspects , 2000 .

[49]  Efthimios Kaxiras,et al.  A Self-Consistent Charge Density-Functional Based Tight-Binding Scheme for Large Biomolecules , 2000 .

[50]  Coral del Val,et al.  PATH: a task for the inference of phylogenies , 2002, Bioinform..

[51]  Thomas Frauenheim,et al.  Energetics and structure of glycine and alanine based model peptides: Approximate SCC-DFTB, AM1 and PM3 methods in comparison with DFT, HF and MP2 calculations , 2001 .

[52]  Sándor Suhai,et al.  Density functional computational thermochemistry: determination of the enthalpy of formation of sulfine, CH2SO, at room temperature , 2000 .

[53]  Sándor Suhai,et al.  Evaluating the formation of salt-bridges: a molecular orbital study , 2000 .

[54]  S. Suhai,et al.  BSSE-Free Description of the Formamide Dimers , 2001 .

[55]  S Suhai,et al.  Neural-network analysis of the vibrational spectra of N-acetyl L-alanyl N'-methyl amide conformational states. , 2001, Physical review. E, Statistical, nonlinear, and soft matter physics.

[56]  S. Suhai,et al.  Toward a BSSE‐free description of strongly interacting systems , 2002 .

[57]  Sándor Suhai,et al.  DFT studies on helix formation in N-acetyl-(L-alanyl)n-N′-methylamide for n=1–20 , 2000 .

[58]  S. Suhai,et al.  Combined quantum chemical and RRKM modeling of the main fragmentation pathways of protonated GGG. II. Formation of b(2), y(1), and y(2) ions. , 2002, Rapid communications in mass spectrometry : RCM.

[59]  P. Lugli,et al.  A simple tight-binding approach to Time-Dependent Density-Functional Response-Theory , 2001 .

[60]  S. Suhai,et al.  Theoretical study of the main fragmentation pathways for protonated glycylglycine. , 2001, Rapid communications in mass spectrometry : RCM.

[61]  Efthimios Kaxiras,et al.  A QM/MM Implementation of the Self-Consistent Charge Density Functional Tight Binding (SCC-DFTB) Method , 2001 .

[62]  S Suhai,et al.  Proton mobility in protonated peptides: a joint molecular orbital and RRKM study. , 2000, Rapid communications in mass spectrometry : RCM.

[63]  Sándor Suhai,et al.  Role and Results of statistical methods in protein fold class prediction , 2001 .