A protein secondary structure prediction scheme for the IBM PC and compatibles. - Stavros J. Hamodrakas (Comput. Appl. Biosci., 1988)

PBM: a software package to create, display and manipulate interactively models of small molecules and proteins on IBM-compatible PCs. - Anastassis Perrakis; C. Constantinides; A. Athanasiades; Stavros J. Hamodrakas (Comput. Appl. Biosci., 1995)

A web server to locate periodicities in a sequence. - C. M. Pasquier; Vasilis J. Promponas; N. J. Varvayannis; Stavros J. Hamodrakas (Bioinform., 1998)

CoPreTHi: A Web tool which combines transmembrane protein segment prediction methods. - Vasilis J. Promponas; G. A. Palaios; C. M. Pasquier; J. S. Hamodrakas; Stavros J. Hamodrakas (Silico Biol., 1998)

CAST: an iterative algorithm for the complexity analysis of sequence tracts. - Vasilis J. Promponas; Anton J. Enright; Sophia Tsoka; David P. Kreil; Christophe Leroy; Stavros J. Hamodrakas; Chris Sander; Christos A. Ouzounis (Bioinform., 2000)

Evaluation of annotation strategies using an entire genome sequence. - Ioannis Iliopoulos; Sophia Tsoka; Miguel A. Andrade; Anton J. Enright; Mark Carroll; Patrick Poullet; Vasilis J. Promponas; Theodore Liakopoulos; Giorgos Palaios; Claude Pasquier; Stavros J. Hamodrakas; Javier Tamames; et al. (Bioinform., 2003)

GeneViTo: Visualizing gene-product functional and structural features in genomic datasets. - Georgios S. Vernikos; Christos G. Gkogkas; Vasilis J. Promponas; Stavros J. Hamodrakas (BMC Bioinform., 2003)

Faster Gradient Descent Training of Hidden Markov Models, Using Individual Learning Rate Adaptation. - Pantelis G. Bagos; Theodore Liakopoulos; Stavros J. Hamodrakas (ICGI, 2004)

TMRPres2D: high quality visual representation of transmembrane protein models. - Ioannis C. Spyropoulos; Theodore Liakopoulos; Pantelis G. Bagos; Stavros J. Hamodrakas (Bioinform., 2004)

A Hidden Markov Model method, capable of predicting and discriminating beta-barrel outer membrane proteins. - Pantelis G. Bagos; Theodore Liakopoulos; Ioannis C. Spyropoulos; Stavros J. Hamodrakas (BMC Bioinform., 2004)

A database for G proteins and their interaction with GPCRs. - Antigoni L. Elefsinioti; Pantelis G. Bagos; Ioannis C. Spyropoulos; Stavros J. Hamodrakas (BMC Bioinform., 2004)

cuticleDB: a relational database of Arthropod cuticular proteins. - Christiana K. Magkrioti; Ioannis C. Spyropoulos; Vassiliki A. Iconomidou; Judith H. Willis; Stavros J. Hamodrakas (BMC Bioinform., 2004)

waveTM: Wavelet-based transmembrane segment prediction. - Evanthia E. Pashou; Zoi I. Litou; Theodore Liakopoulos; Stavros J. Hamodrakas (Silico Biol., 2004)

PRED-TMBB: a web server for predicting the topology of ?barrel outer membrane proteins. - Pantelis G. Bagos; Theodore Liakopoulos; Ioannis C. Spyropoulos; Stavros J. Hamodrakas (Nucleic Acids Res., 2004)

PRED-GPCR: GPCR recognition and family classification server. - Panagiotis K. Papasaikas; Pantelis G. Bagos; Zoi I. Litou; Vasilis J. Promponas; Stavros J. Hamodrakas (Nucleic Acids Res., 2004)

Prediction of the coupling specificity of GPCRs to four families of G-proteins using hidden Markov models and artificial neural networks. - Nikolaos G. Sgourakis; Pantelis G. Bagos; Stavros J. Hamodrakas (Bioinform., 2005)

Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method. - Pantelis G. Bagos; Theodore Liakopoulos; Stavros J. Hamodrakas (BMC Bioinform., 2005)

N-terminal sequence-based prediction of subcellular location. - Evangelia Petsalakis; Pantelis G. Bagos; Zoi I. Litou; Stavros J. Hamodrakas (BMC Bioinform., 2005)

A method for the prediction of GPCRs coupling specificity to G-proteins using refined profile Hidden Markov Models. - Nikolaos G. Sgourakis; Pantelis G. Bagos; Panagiotis K. Papasaikas; Stavros J. Hamodrakas (BMC Bioinform., 2005)

Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins. - Pantelis G. Bagos; Theodore D. Liakopoulos; Stavros J. Hamodrakas (BMC Bioinform., 2006)

PredSL: A Tool for the N-terminal Sequence-based Prediction of Protein Subcellular Localization. - Evangelia Petsalaki; Pantelis G. Bagos; Zoi I. Litou; Stavros J. Hamodrakas (Genom. Proteom. Bioinform., 2006)

gpDB: a database of GPCRs, G-proteins, effectors and their interactions. - Margarita C. Theodoropoulou; Pantelis G. Bagos; Ioannis C. Spyropoulos; Stavros J. Hamodrakas (Bioinform., 2008)

Prediction of Cell Wall Sorting Signals in Gram-Positive bacteria with a Hidden Markov Model: Application to Complete genomes. - Zoi I. Litou; Pantelis G. Bagos; Konstantinos D. Tsirigos; Theodore D. Liakopoulos; Stavros J. Hamodrakas (J. Bioinform. Comput. Biol., 2008)

How Many 3D Structures Do We Need to Train a Predictor? - Pantelis G. Bagos; Georgios N. Tsaousis; Stavros J. Hamodrakas (Genom. Proteom. Bioinform., 2009)

GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques. - Venkata P. Satagopam; Margarita C. Theodoropoulou; Christos K. Stampolakis; Georgios A. Pavlopoulos; Nikolaos Papandreou; Pantelis G. Bagos; Reinhard Schneider 002; Stavros J. Hamodrakas (Database J. Biol. Databases Curation, 2010)

ExTopoDB: a database of experimentally derived topological models of transmembrane proteins. - Georgios N. Tsaousis; Konstantinos D. Tsirigos; Xanthi D. Andrianou; Theodore D. Liakopoulos; Pantelis G. Bagos; Stavros J. Hamodrakas (Bioinform., 2010)

OMPdb: a database of β-barrel outer membrane proteins from Gram-negative bacteria. - Konstantinos D. Tsirigos; Pantelis G. Bagos; Stavros J. Hamodrakas (Nucleic Acids Res., 2011)

CW-PRED: A HMM-Based Method for the Classification of Cell Wall-Anchored Proteins of Gram-Positive Bacteria. - Danai K. Fimereli; Konstantinos D. Tsirigos; Zoi I. Litou; Theodore D. Liakopoulos; Pantelis G. Bagos; Stavros J. Hamodrakas (SETN, 2012)

mpMoRFsDB: a database of molecular recognition features in membrane proteins. - Foivos Gypas; Georgios N. Tsaousis; Stavros J. Hamodrakas (Bioinform., 2013)

Molecular dynamics simulations and structure-based network analysis reveal structural and functional aspects of G-protein coupled receptor dimer interactions. - Fotis A. Baltoumas; Margarita C. Theodoropoulou; Stavros J. Hamodrakas (J. Comput. Aided Mol. Des., 2016)

A β-solenoid model of the Pmel17 repeat domain: insights to the formation of functional amyloid fibrils. - Nikolaos N. Louros; Fotis A. Baltoumas; Stavros J. Hamodrakas; Vassiliki A. Iconomidou (J. Comput. Aided Mol. Des., 2016)

Structural characterization and molecular dynamics simulations of the caprine and bovine solute carrier family 11 A1 (SLC11A1). - Kostas A. Triantaphyllopoulos; Fotis A. Baltoumas; Stavros J. Hamodrakas (J. Comput. Aided Mol. Des., 2019)

The gram-negative outer membrane modeler: Automated building of lipopolysaccharide-rich bacterial outer membranes in four force fields. - Fotis A. Baltoumas; Stavros J. Hamodrakas; Vassiliki A. Iconomidou (J. Comput. Chem., 2019)

OMPdb: A Global Hub of Beta-Barrel Outer Membrane Proteins. - Ahmed F. Roumia; Konstantinos D. Tsirigos; Margarita C. Theodoropoulou; Ioannis A. Tamposis; Stavros J. Hamodrakas; Pantelis G. Bagos (Frontiers Bioinform., 2021)

The human GPCR signal transduction network. - Panagiota I. Kontou; Athanasia Pavlopoulou; Niki L. Dimou; Margarita C. Theodoropoulou; Georgia Braliou; Georgios N. Tsaousis; Georgios A. Pavlopoulos; Stavros J. Hamodrakas; Pantelis G. Bagos (Netw. Model. Anal. Health Informatics Bioinform., 2021)