Search filters

List of works by Stavros J Hamodrakas

A Hidden Markov Model method, capable of predicting and discriminating beta-barrel outer membrane proteins

scientific article

A common 'aggregation-prone' interface possibly participates in the self-assembly of human zona pellucida proteins.

scientific article

A consensus method for the prediction of 'aggregation-prone' peptides in globular proteins

scientific article

A database for G proteins and their interaction with GPCRs

scientific article

A method for the prediction of GPCRs coupling specificity to G-proteins using refined profile Hidden Markov Models

scientific article

A possible structural model of members of the CPF family of cuticular proteins implicating binding to components other than chitin.

scientific article

A structural model of the chitin-binding domain of cuticle proteins

scientific article published in November 2002

A β-solenoid model of the Pmel17 repeat domain: insights to the formation of functional amyloid fibrils.

scientific article

ANTISOMA: A Computational Pipeline for the Reduction of the Aggregation Propensity of Monoclonal Antibodies

scientific article published on 01 January 2020

Acquisition through horizontal gene transfer of plasmid pSMA198 by Streptococcus macedonicus ACA-DC 198 points towards the dairy origin of the species

scientific article

Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins

scientific article published on 5 April 2006

Amyloid fibril formation propensity is inherent into the hexapeptide tandemly repeating sequence of the central domain of silkmoth chorion proteins of the A-family

scientific article published on 5 September 2006

An N-terminal pro-atrial natriuretic peptide (NT-proANP) 'aggregation-prone' segment involved in isolated atrial amyloidosis.

scientific article published on 9 November 2013

An amyloidogenic determinant in N-terminal pro-brain natriuretic peptide (NT-proBNP): Implications for cardiac amyloidoses

scientific article published on 25 July 2011

Analysis of Molecular Recognition Features (MoRFs) in membrane proteins

scientific article published on 15 January 2013

Analysis of Single-Nucleotide Polymorphisms in Human Voltage-Gated Ion Channels

scientific article published on 01 April 2019

Chameleon 'aggregation-prone' segments of apoA-I: A model of amyloid fibrils formed in apoA-I amyloidosis

scientific article published on 3 June 2015

Comparative genomics of the dairy isolate Streptococcus macedonicus ACA-DC 198 against related members of the Streptococcus bovis/Streptococcus equinus complex

scientific article

Consensus prediction of amyloidogenic determinants in amyloid fibril-forming proteins

scientific article published on 25 March 2007

CutProtFam-Pred: detection and classification of putative structural cuticular proteins from sequence alone, based on profile hidden Markov models

scientific article

Cytokine gene polymorphisms in periodontal disease: a meta-analysis of 53 studies including 4178 cases and 4590 controls

scientific article published on 31 July 2008

Dogfish egg case structural studies by ATR FT-IR and FT-Raman spectroscopy

scientific article published on 19 January 2007

Drosophila cuticular proteins with the R&R Consensus: annotation and classification with a new tool for discriminating RR-1 and RR-2 sequences

scientific article published on 19 March 2007

Evaluation of annotation strategies using an entire genome sequence

scientific article

Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method

scientific article

ExTopoDB: a database of experimentally derived topological models of transmembrane proteins

article

Exploring Amyloidogenicity of Clusterin: A Structural and Bioinformatics Analysis.

scientific article

Exploring the 'aggregation-prone' core of human Cystatin C: A structural study

scientific article published on 30 July 2015

FT-Raman spectroscopy as diagnostic tool of Congo red binding to amyloids

scientific article

Fcgamma receptor polymorphisms and their association with periodontal disease: a meta-analysis

scientific article published on March 2010

GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques

scientific article

GeneViTo: visualizing gene-product functional and structural features in genomic datasets

scientific article

GprotPRED: Annotation of Gα, Gβ and Gγ subunits of G-proteins using profile Hidden Markov Models (pHMMs) and application to proteomes

scientific article published on 4 February 2016

HMMpTM: improving transmembrane protein topology prediction using phosphorylation and glycosylation site prediction

scientific article

Haloadaptation: insights from comparative modeling studies of halophilic archaeal DHFRs.

scientific article published on 19 June 2007

How many 3D structures do we need to train a predictor?

scientific article

Identification of a novel 'aggregation-prone'/'amyloidogenic determinant' peptide in the sequence of the highly amyloidogenic human calcitonin

scientific article

Interactions of the α-subunits of heterotrimeric G-proteins with GPCRs, effectors and RGS proteins: A critical review and analysis of interacting surfaces, conformational shifts, structural diversity and electrostatic potentials ⬇️

scientific article published on March 21, 2013

Intrinsic aggregation propensity of the CsgB nucleator protein is crucial for curli fiber formation.

scientific article published on 28 May 2016

MBPpred: Proteome-wide detection of membrane lipid-binding proteins using profile Hidden Markov Models.

scientific article published on 2 April 2016

Meeting report: the seventh conference of the hellenic society for computational biology and bioinformatics.

scientific article published on 16 June 2013

Methylene tetrahydrofolate reductase gene polymorphisms and their association with methotrexate toxicity: a meta-analysis

scientific article published on February 2012

Mining databases for protein aggregation: a review

scientific article published on 18 July 2017

Molecular dynamics simulations and structure-based network analysis reveal structural and functional aspects of G-protein coupled receptor dimer interactions.

scientific article published on 27 June 2016

No evidence for association of CTLA-4 gene polymorphisms with the risk of developing multiple sclerosis: a meta-analysis

article

OMPdb: a database of {beta}-barrel outer membrane proteins from Gram-negative bacteria

scientific article

PRED-TMBB: a web server for predicting the topology of beta-barrel outer membrane proteins

scientific article

Phoenix 100 versus Vitek 2 in the identification of gram-positive and gram-negative bacteria: a comprehensive meta-analysis

scientific article

PredSL: a tool for the N-terminal sequence-based prediction of protein subcellular localization

scientific article published on February 2006

Predicting Alpha Helical Transmembrane Proteins Using HMMs.

scientific article published on January 2017

Predicting Beta Barrel Transmembrane Proteins Using HMMs

scientific article

Prediction of cell wall sorting signals in gram-positive bacteria with a hidden markov model: application to complete genomes

scientific article published in April 2008

Prediction of lipoprotein signal peptides in Gram-positive bacteria with a Hidden Markov Model

scientific article

Prediction of the coupling specificity of GPCRs to four families of G-proteins using hidden Markov models and artificial neural networks

scientific article published on 20 September 2005

Structural analysis of peptide-analogues of human Zona Pellucida ZP1 protein with amyloidogenic properties: insights into mammalian Zona Pellucida formation

scientific article

Structural characterization and molecular dynamics simulations of the caprine and bovine solute carrier family 11 A1 (SLC11A1)

scientific article published on 12 December 2018

Structural studies and cytotoxicity assays of "aggregation-prone" IAPP(8-16) and its non-amyloidogenic variants suggest its important role in fibrillogenesis and cytotoxicity of human amylin

scientific article published on May 2015

Structural studies of "aggregation-prone" peptide-analogues of teleostean egg chorion ZPB proteins

scientific article published in November 2014

TMRPres2D: high quality visual representation of transmembrane protein models

scientific article

The GNB3 C825T polymorphism and essential hypertension: a meta-analysis of 34 studies including 14,094 cases and 17,760 controls

scientific article published in March 2007

The amyloid interactome: Exploring protein aggregation

scientific article published on March 2017

The gram-negative outer membrane modeler: Automated building of lipopolysaccharide-rich bacterial outer membranes in four force fields

scientific article published on 19 March 2019

The human plasma membrane peripherome: visualization and analysis of interactions.

scientific article

The pentapeptide LQVVR plays a pivotal role in human cystatin C fibrillization

scientific article

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

scientific article published on 18 February 2011

Tracking the amyloidogenic core of IAPP amyloid fibrils: Insights from micro-Raman spectroscopy.

scientific article published on 5 June 2017

Unique features of the structural model of 'hard' cuticle proteins: implications for chitin-protein interactions and cross-linking in cuticle

scientific article published on 8 March 2005

Unraveling the aggregation propensity of human insulin C-peptide

scientific article published on 3 June 2016

cuticleDB: a relational database of Arthropod cuticular proteins

scientific article

gpDB: a database of GPCRs, G-proteins, effectors and their interactions

scientific article published on 25 April 2008

mpMoRFsDB: a database of molecular recognition features in membrane proteins

scientific article published on 26 July 2013

waveTM: wavelet-based transmembrane segment prediction.

scientific article published in January 2004

αCGRP, another amyloidogenic member of the CGRP family.

scientific article published in March 2018

Paulina is supported by:

About Paulina

Help