Stavros J. Hamodrakas - researchr alias

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Viewing Publication 1 - 35 from 35

2021

2019

The gram-negative outer membrane modeler: Automated building of lipopolysaccharide-rich bacterial outer membranes in four force fieldsFotis A. Baltoumas, Stavros J. Hamodrakas, Vassiliki A. Iconomidou. jcc, 40(18):1727-1734, 2019. [doi]

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. jcamd, 33(2):265-285, 2019. [doi]

2016

Molecular dynamics simulations and structure-based network analysis reveal structural and functional aspects of G-protein coupled receptor dimer interactionsFotis A. Baltoumas, Margarita C. Theodoropoulou, Stavros J. Hamodrakas. jcamd, 30(6):489-512, 2016. [doi]

A β-solenoid model of the Pmel17 repeat domain: insights to the formation of functional amyloid fibrilsNikolaos N. Louros, Fotis A. Baltoumas, Stavros J. Hamodrakas, Vassiliki A. Iconomidou. jcamd, 30(2):153-164, 2016. [doi]

2013

mpMoRFsDB: a database of molecular recognition features in membrane proteinsFoivos Gypas, Georgios N. Tsaousis, Stavros J. Hamodrakas. bioinformatics, 29(19):2517-2518, 2013. [doi]

2012

CW-PRED: A HMM-Based Method for the Classification of Cell Wall-Anchored Proteins of Gram-Positive BacteriaDanai K. Fimereli, Konstantinos D. Tsirigos, Zoi I. Litou, Theodore D. Liakopoulos, Pantelis G. Bagos, Stavros J. Hamodrakas. setn 2012: 285-290 [doi]

2011

OMPdb: a database of β-barrel outer membrane proteins from Gram-negative bacteriaKonstantinos D. Tsirigos, Pantelis G. Bagos, Stavros J. Hamodrakas. nar, 39(Database-Issue):324-331, 2011. [doi]

2010

2009

How Many 3D Structures Do We Need to Train a Predictor?Pantelis G. Bagos, Georgios N. Tsaousis, Stavros J. Hamodrakas. gpb, 7(3):128-137, 2009. [doi]

2008

Prediction of Cell Wall Sorting Signals in Gram-Positive bacteria with a Hidden Markov Model: Application to Complete genomesZoi I. Litou, Pantelis G. Bagos, Konstantinos D. Tsirigos, Theodore D. Liakopoulos, Stavros J. Hamodrakas. jbcb, 6(2):387-401, 2008. [doi]

gpDB: a database of GPCRs, G-proteins, effectors and their interactionsMargarita C. Theodoropoulou, Pantelis G. Bagos, Ioannis C. Spyropoulos, Stavros J. Hamodrakas. bioinformatics, 24(12):1471-1472, 2008. [doi]

2006

Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteinsPantelis G. Bagos, Theodore D. Liakopoulos, Stavros J. Hamodrakas. bmcbi, 7:189, 2006. [doi]

PredSL: A Tool for the N-terminal Sequence-based Prediction of Protein Subcellular LocalizationEvangelia Petsalaki, Pantelis G. Bagos, Zoi I. Litou, Stavros J. Hamodrakas. gpb, 4(1):48-55, 2006. [doi]

2005

Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction methodPantelis G. Bagos, Theodore Liakopoulos, Stavros J. Hamodrakas. bmcbi, 6:7, 2005. [doi]

N-terminal sequence-based prediction of subcellular locationEvangelia I. Petsalakis, Pantelis G. Bagos, Zoi I. Litou, Stavros J. Hamodrakas. bmcbi, 6(S-3), 2005. [doi]

Prediction of the coupling specificity of GPCRs to four families of G-proteins using hidden Markov models and artificial neural networksNikolaos G. Sgourakis, Pantelis G. Bagos, Stavros J. Hamodrakas. bioinformatics, 21(22):4101-4106, 2005. [doi]

A method for the prediction of GPCRs coupling specificity to G-proteins using refined profile Hidden Markov ModelsNikolaos G. Sgourakis, Pantelis G. Bagos, Panagiotis K. Papasaikas, Stavros J. Hamodrakas. bmcbi, 6:104, 2005. [doi]

2004

PRED-TMBB: a web server for predicting the topology of ?barrel outer membrane proteinsPantelis G. Bagos, Theodore Liakopoulos, Ioannis C. Spyropoulos, Stavros J. Hamodrakas. nar, 32(Web-Server-Issue):400-404, 2004.

A Hidden Markov Model method, capable of predicting and discriminating beta-barrel outer membrane proteinsPantelis G. Bagos, Theodore Liakopoulos, Ioannis C. Spyropoulos, Stavros J. Hamodrakas. bmcbi, 5:29, 2004. [doi]

Faster Gradient Descent Training of Hidden Markov Models, Using Individual Learning Rate AdaptationPantelis G. Bagos, Theodore Liakopoulos, Stavros J. Hamodrakas. icgi 2004: 40-52 [doi]

A database for G proteins and their interaction with GPCRsAntigoni L. Elefsinioti, Pantelis G. Bagos, Ioannis C. Spyropoulos, Stavros J. Hamodrakas. bmcbi, 5:208, 2004. [doi]

cuticleDB: a relational database of Arthropod cuticular proteinsChristiana K. Magkrioti, Ioannis C. Spyropoulos, Vassiliki A. Iconomidou, Judith H. Willis, Stavros J. Hamodrakas. bmcbi, 5:138, 2004. [doi]

PRED-GPCR: GPCR recognition and family classification serverPanagiotis K. Papasaikas, Pantelis G. Bagos, Zoi I. Litou, Vassilis J. Promponas, Stavros J. Hamodrakas. nar, 32(Web-Server-Issue):380-382, 2004.

waveTM: Wavelet-based transmembrane segment predictionEvanthia E. Pashou, Zoi I. Litou, Theodore Liakopoulos, Stavros J. Hamodrakas. isb, 4:127-131, 2004. [doi]

TMRPres2D: high quality visual representation of transmembrane protein modelsIoannis C. Spyropoulos, Theodore Liakopoulos, Pantelis G. Bagos, Stavros J. Hamodrakas. bioinformatics, 20(17):3258-3260, 2004. [doi]

2003

2000

CAST: an iterative algorithm for the complexity analysis of sequence tractsVassilis J. Promponas, Anton J. Enright, Sophia Tsoka, David P. Kreil, Christophe Leroy, Stavros J. Hamodrakas, Chris Sander, Christos A. Ouzounis. bioinformatics, 16(10):915-922, 2000.

1998

A web server to locate periodicities in a sequenceC. M. Pasquier, Vassilis J. Promponas, N. J. Varvayannis, Stavros J. Hamodrakas. bioinformatics, 14(8):749-750, 1998.

CoPreTHi: A Web tool which combines transmembrane protein segment prediction methodsVassilis J. Promponas, G. A. Palaios, C. M. Pasquier, J. S. Hamodrakas, Stavros J. Hamodrakas. isb, 1:14, 1998. [doi]

1995

PBM: a software package to create, display and manipulate interactively models of small molecules and proteins on IBM-compatible PCsA. Perrakis, C. Constantinides, A. Athanasiades, Stavros J. Hamodrakas. bioinformatics, 11(2):141-145, 1995.

1988

A protein secondary structure prediction scheme for the IBM PC and compatiblesStavros J. Hamodrakas. bioinformatics, 4(4):473-477, 1988.

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