The Protein World

Bioinformatics Symposium and Poster Session

Oral presentations: July 5, 15:30-18:30 (Room 1a and optionally Room 1b)
Poster presentations: July 5, 13:30-15:30 (Building-A, Section 4)

Chairpersons

• Sándor Pongor (Trieste, Italy)
• Zoltan N. Oltvai (Pittsburgh, USA)

Oral presentations

• A3-002 15:30-16:00: Zoltan N. Oltvai (Pittsburgh, United States of America):
  Functional organization of transcriptional-regulatory networks Abstract
• O1-183 16:00-16:30: Sándor Pongor (Trieste, Italy):
  Multiple weak hits confuse transcriptional regulatory networks Abstract
• A3-003 16:30-17:00: Piotr Zielenkiewicz (Warsaw, Poland):
  The evolutionary history of the eukaryotic interactome Abstract
• 17:00-17:20 —————-Coffee break—————-
• A3-004 17:20-17:50: Jordi Villŕ-Freixa (Barcelona, Spain):
  Per residue characterization of protein-protein interfaces: a relationship between stability and functionality? Abstract
• A3-005 17:50-18:10: Janusz Bujnicki (Warsaw, Poland, EMBO Young Investigator Lecture):
  Protein structure prediction by the combination of fold-recognition with de novo folding Abstract

Poster presentations

• A3-007P Clara Allayous (Pointe-ŕ-Pitre, Guadeloupe (France)):
  Decision trees: a statistical method to explain the triggering mechanisms of acute splenic sequestration crisis in sickle cell disease. Abstract
• A3-008P Petra Aradi (Budapest, Hungary):
  Origin and development of the genetic code: Is there a code in the codon? Abstract
• A3-009P Joăo Pedro Abecasis (Lisboa, Portugal):
  A C++ code library for metabolic modeling Abstract
• A3-010P Abdelwaheb Benothmane (Monastir, Tunisia):
  Mitochondrial DNA phylogeny of Androctonus Ehrenberg, 1828 (Scorpiones: Buthidae) and its bearing on taxonomy and biogeography in Tunisia Abstract
• A3-011P Andreas Böhm (Würzburg, Germany):
  A clustering solution for distributed data analysis in mass spectrometry – paOla Abstract
• A3-012P Balázs Benyó (Győr, Hungary):
  Searching sequences in protein databases generated by overlapping translation Abstract
• A3-013P Alexander Chernorudskiy (Dzerzhinsk, Russia):
  Spatial limitations caused by ubiquitylation: analysis of the 3D model of yeast peroxisomal citrate synthase-ubiquitin complex Abstract
• A3-014P Siavoush Dastmalchi (Tabriz, Iran):
  Prediction of the rotational orientation of transmembrane helices of membrane proteins using a new structurally derived scale Abstract
• A3-015P Benoit Dessailly (Bruxelles, Belgium):
  Large-scale analysis of patches of contiguous destabilizing residues in proteins of known three-dimensional structure: towards functional sites prediction Abstract
• A3-016P Gergely Fördős (Budapest, Hungary):
  An analytical tool to detect and visualize residue co-locations in protein and nucleic acid structures Abstract
• A3-017P Nathalie Farriol-Mathis (Geneva 4, Switzerland):
  Annotation of post-translational modifications in Swiss-Prot and their effect in cell context Abstract
• A3-019P László Galgóczy (Szeged, Hungary):
  Sequence comparison of high-affinity iron permeases (FTR1) from different zygomycetous fungi Abstract
• A3-020P Janosch Hennig (Linköping, Sweden):
  High-order structure probing for misbehaving proteins and high-throughput approaches Abstract
• A3-021P Jing Huang (Wuhan, PR China):
  Using multi-properties of protein in predicting protein subcellular localization Abstract
• A3-022P Ursula Hinz (Geneva, Switzerland):
  Uniprot & Swiss-Prot: providing a link between protein sequences and state of the art knowledge Abstract
• A3-023P Sándor Kocsubé (Szeged, Hungary):
  Identification of genes taking part in siderophore biosynthesis in the genome of Fusarium graminearum Abstract
• A3-024P Eleonora Kurtenbach (Rio De Janeiro, Brazil):
  Heterologous expression and characterization of S. cerevisiae unknown proteins induced by hydrostatic pressure Abstract
• A3-026P Ivana Lescic (Zagreb, Croatia):
  3D-Structure features of novel GDSL-enzyme by bioinformatic methods and mass spectrometry Abstract
• A3-027P Damien Lieberherr (Geneva, Switzerland):
  The Plant Proteome Annotation Program (PPAP) of UniProtKB/Swiss-Prot Abstract
• A3-028P Marc Lensink (Brussels, Belgium):
  Prediction of protein functional sites by energetic stability calculations Abstract
• A3-029P Istvan Miklos (Budapest, Hungary):
  Statistical alignment of retropseudogenes and their functional paralogs via a common ancestor Abstract
• A3-030P Martin Lee Miller (Lyngby, Denmark):
  NetPhosK – Prediction of kinase-specific phosphorylation from sequence and sequence-derived features Abstract
• A3-031P Carri-Lyn Mead (Vancouver, Canada):
  Investigating lattice structure for Inverse Protein Folding Abstract
• A3-032P Yoshiaki Minezaki (Mishima, Japan):
  Comparative genomics of transcription factors Abstract
• A3-033P Peter Nagy (Budapest, Hungary):
  A statistical study on the distribution and pattern (structure) of 1200 different human repeat types using a newly developed tool (SeqRep) and a Compressed Repeat Database (CompRepDB) Abstract
• A3-034P Josep Maria Orellana (Tarragona, Spain):
  Arrangement of sequences in the gamma-proteobacteria replication origin Abstract
• A3-035P Sergio Oyama Jr. (Campinas, Brazil):
  Docking of the scorpion toxin α-KTx_12.1 to K⁺ channels investigated by molecular dynamics simulations Abstract
• A3-037P Sarolta Pilbak (Budapest, Hungary):
  QM/MM calculations on the rearrangement reaction of isobutyryl-CoA mutase Abstract
• A3-038P Tamás Ponyi (Bp, Hungary):
  Computer analysis of glycosyl hydrolases Abstract
• A3-039P Ansgar Philippsen (Basel, Switzerland):
  Visualizing structural biology using DINO Abstract
• A3-040P Karine Robbe (Cambridge, United Kingdom):
  IntAct: an open-source database system and analysis tools for protein interaction data Abstract
• A3-042P Gabor Szatzker (Budapest, Hungary):
  Enantioselectivity in Candida antarctica lipase B reaction: transition states calculated by QM/MM methods Abstract
• A3-043P Zinovia Spyranti (Patras, Greece):
  Enzyme-substrate interaction through docking stimulation – Part II. Binding properties of vasopeptidase inhibitors studied in complexes with Zn(II) metallopeptidases involved in blood pressure regulation Abstract
• A3-044P Stefan Tomiuk (Cologne, Germany):
  A method for enhancing the significance of short linear motif matches Abstract
• A3-046P Alexander Vener (Linkoping, Sweden):
  Vectorial proteomics of biological membranes Abstract
• A3-047P Grzegorz Wieczorek (Warszawa, Poland):
  A theoretical approach to the influence of macromolecular crowding on reaction rates Abstract
• A3-048P Bogdan Walkowiak (Lodz, Poland):
  Interaction of endothelial cells with selected biomaterials causes changes in protein expression profile Abstract
• A3-049P Yu Zhang (Lyngby, Denmark):
  Identification of the C-terminal signal peptides for GPI modification and prediction of the cleavage sites Abstract
• A3-050P Rene Zahedi (Würzburg, Germany):
  Towards an extensive proteome analysis of platelet membranes Abstract
• A3-051P Arnon Paz (Haifa, Israel):
  Biased purine frequency and polypurine tracts in mRNA sequences of the proteins belong to information processing: comparisons within Prokarya and Eukarya Abstract