The Biophysics and Bioinformatics Laboratory of the Department of Cell Biology and Biophysics of the University of Athens focuses over the last three decades on research related to the elucidation of the principles governing protein structure and function, under the supervision of Professor Stavros J. Hamodrakas.
In particular, original research is carried out along two main axes:
1. Algorithm development for the prediction of protein structure, function and interactions from amino acid sequence as well as construction of relevant databases. (more)
2. Application of a variety of Biophysical methods and techniques for protein structure determination and for structural studies of complex, physiologically important, Biological tissues such as insect chorion and cuticle.
More than 15 individuals (including post-doctoral researchers, PhD students, MSc and undergraduate students) are currently involved in several ongoing research projects.
Apart from research, our lab offers undergraduate courses in Bioinformatics and Molecular Biophysics, which are elective for the degrees (BSc) in Biology (Faculty of Biology) and Physics (Faculty of Physics) of the University of Athens.
At the same time, our lab is actively involved in the organization and co-ordination of the MSc Programme in Bioinformatics of the Faculty of Biology. (more)
2013: AMYL-PRED 2: A Consensus Method for Amyloid Propensity Prediction.
2013: LepChorionDB: Lepidoptera chorion protein database./
Protein aggregation and amyloid fibril formation prediction software from primary sequence: towards controlling the formation of bacterial inclusion bodies.
The silkmoth eggshell as a natural amyloid shield for the safe development of insect oocyte and embryo: Insights from studies of silkmoth chorion protein peptide-analogues of the B family.
OMPdb: A database of ß-barrel outer membrane proteins from Gram negative bacteria.
ExTopoDB: A database of experimentally derived topological models of transmembrane proteins.
Amyloidogenic determinants are usually not buried.
gpDB: a database of GPCRs, G-proteins, effectors and their interactions.
Prediction of the coupling specificity of GPCRs to four families of G-proteins using hidden Markov models and artificial neural networks.
2005: A method for the prediction of GPCRs coupling specificity to G-proteins using refined profile Hidden Markov Models.
Evaluation of methods for predicting the topology of β-barrel outer membrane proteins and a consensus prediction method.
Unique features of the structural model of hard cuticle proteins: implications for chitin-protein interactions and cross-linking in cuticle.
2005: Cuticular Proteins in 'Comprehensive Insect Science'.
LepChorionDB: Lepidoptera chorion protein database.
AMYL-PRED 2: A Consensus Method for Amyloid Propensity Prediction.
ExTopoDB: a publicly accessible database of experimentally derived topological models of transmembrane proteins.
OMPdb: A database of ß-barrel outer membrane proteins from Gram-negative bacteria.
Human-gpDB: database of human GPCRs, G-proteins, Effectors and their interactions.
HMM-TM: A Hidden Markov Model method for the topology prediction of
alpha-helical membrane proteins that incorporates experimentally derived topological information.
hPATM: heuristic pairwise alignment for transmembrane proteins.
PRED-COUPLE 2: A tool that predicts the coupling specificity of G-protein coupled receptors to G-proteins.
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