List of works - Istvan Simon

A word of caution about biological inference - Revisiting cysteine covalent state predictions.

scientific article

ANCHOR: web server for predicting protein binding regions in disordered proteins.

scientific article published on 28 August 2009

Active site residue involvement in monoamine or diamine oxidation catalysed by pea seedling amine oxidase

scientific article published on 01 March 2011

Analysis of Heterodimeric "Mutual Synergistic Folding"-Complexes

scientific article published on 16 October 2019

CMWeb: an interactive on-line tool for analysing residue-residue contacts and contact prediction methods.

scientific article

Combination of 2D/3D ligand-based similarity search in rapid virtual screening from multimillion compound repositories. Selection and biological evaluation of potential PDE4 and PDE5 inhibitors.

scientific article

Combination of Pharmacophore Matching, 2D Similarity Search, and In Vitro Biological Assays in the Selection of Potential 5-HT6 Antagonists from Large Commercial Repositories

scientific article published on 30 March 2015

DIBS: a repository of disordered binding sites mediating interactions with ordered proteins.

scientific article published in February 2018

Disorder and sequence repeats in hub proteins and their implications for network evolution.

scientific article published in November 2006

Disordered binding regions and linear motifs--bridging the gap between two models of molecular recognition.

scientific article

Disordered tails of homeodomains facilitate DNA recognition by providing a trade-off between folding and specific binding

scientific article published on 01 October 2009

Dynamic protein–DNA recognition: beyond what can be seen ⬇️

scientific article published on May 27, 2011

Electrostatic versus nonelectrostatic effects in DNA sequence discrimination by divalent ions Mg2+ and Mn2+

scientific article published on 12 May 2007

Flexibility of prolyl oligopeptidase: molecular dynamics and molecular framework analysis of the potential substrate pathways.

scientific article published in August 2005

Flexible segments modulate co-folding of dUTPase and nucleocapsid proteins

scientific article

Functionally and structurally relevant residues of enzymes: are they segregated or overlapping?

scientific article

Identification of potential glutaminyl cyclase inhibitors from lead-like libraries by in silico and in vitro fragment-based screening

scientific article

Interfacial water as a "hydration fingerprint" in the noncognate complex of BamHI.

scientific article

Investigation of protein folding: Uneven distribution of point mutations along polypeptide chains ⬇️

scientific article published on November 21, 1979

Is there a biological cost of protein disorder? Analysis of cancer-associated mutations

article

Local structural disorder imparts plasticity on linear motifs.

scientific article

MFIB: a repository of protein complexes with mutual folding induced by binding.

scientific article published on 3 August 2017

Macromolecular Interactions of Disordered Proteins

scientific article published on 13 January 2020

Malleable machines in transcription regulation: the mediator complex

scientific article

Membrane topology of human ABC proteins.

scientific article

Metal-binding sites at the active site of restriction endonuclease BamHI can conform to a one-ion mechanism

scientific article published on 01 January 2007

Molecular Principles of the Interactions of Disordered Proteins

article

Nucleotide pyrophosphatase employs a P-loop-like motif to enhance catalytic power and NDP/NTP discrimination.

scientific article

PDBTM: Protein Data Bank of transmembrane proteins after 8 years

scientific article

PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank

scientific article

Phosphorylation-induced transient intrinsic structure in the kinase-inducible domain of CREB facilitates its recognition by the KIX domain of CBP

scientific article published on 01 August 2006

Physical Background of the Disordered Nature of "Mutual Synergetic Folding" Proteins

scientific article published on 26 October 2018

Possible mechanism for the dynamic stabilization of protein structure ⬇️

scientific article published on June 21, 1981

Predicting redox state of cysteines in proteins.

scientific article

Prevalent structural disorder in E. coli and S. cerevisiae proteomes.

scientific article published on August 2006

Probing the two-metal ion mechanism in the restriction endonuclease BamHI.

scientific article published on 17 November 2007

Proteins with complex architecture as potential targets for drug design: a case study of Mycobacterium tuberculosis

scientific article

QM/MM simulation of liquid water with an adaptive quantum region

scientific article published on 16 November 2011

Rod models of DNA: sequence-dependent anisotropic elastic modelling of local bending phenomena

scientific article published on 01 September 1998

Role of base flipping in specific recognition of damaged DNA by repair enzymes.

scientific article

Role of stabilization centers in 4 helix bundle proteins

scientific article published on 01 August 2002

SCide: identification of stabilization centers in proteins ⬇️

scientific article published on May 1, 2003

Sequence and Structure Properties Uncover the Natural Classification of Protein Complexes Formed by Intrinsically Disordered Proteins via Mutual Synergistic Folding ⬇️

scientific article published on 01 November 2019

Sequential, Structural and Functional Properties of Protein Complexes Are Defined by How Folding and Binding Intertwine

scientific article published on 12 August 2019

Series of concentration-induced phase transitions in cholesterol/phosphatidylcholine mixtures.

scientific article published on June 2013

Stabilization centers in proteins: identification, characterization and predictions.

scientific article published in October 1997

Systematic analysis of somatic mutations driving cancer: uncovering functional protein regions in disease development.

scientific article published on 5 May 2016

TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter.

scientific article published in January 2004

TOPDB: topology data bank of transmembrane proteins

scientific article (publication date: 2008)

The BiSearch web server

scientific article

The energy gap as a universal reaction coordinate for the simulation of chemical reactions

scientific article published on 01 June 2009

The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins.

scientific article published in April 2005

The role of DNA bending in Cro protein-DNA interactions ⬇️

scientific article published on December 1, 1997

The role of dimerization in prion replication

scientific article

The role of hydrophobic microenvironments in modulating pKa shifts in proteins.

scientific article

Topology Prediction of Helical Transmembrane Proteins: How Far Have We Reached? ⬇️

scientific article published on November 1, 2010

Transmembrane proteins in the Protein Data Bank: identification and classification.

scientific article

List of works by Istvan Simon

A word of caution about biological inference - Revisiting cysteine covalent state predictions.

ANCHOR: web server for predicting protein binding regions in disordered proteins.

Active site residue involvement in monoamine or diamine oxidation catalysed by pea seedling amine oxidase

Analysis of Heterodimeric "Mutual Synergistic Folding"-Complexes

CMWeb: an interactive on-line tool for analysing residue-residue contacts and contact prediction methods.

Combination of 2D/3D ligand-based similarity search in rapid virtual screening from multimillion compound repositories. Selection and biological evaluation of potential PDE4 and PDE5 inhibitors.

Combination of Pharmacophore Matching, 2D Similarity Search, and In Vitro Biological Assays in the Selection of Potential 5-HT6 Antagonists from Large Commercial Repositories

DIBS: a repository of disordered binding sites mediating interactions with ordered proteins.

Disorder and sequence repeats in hub proteins and their implications for network evolution.

Disordered binding regions and linear motifs--bridging the gap between two models of molecular recognition.

Disordered tails of homeodomains facilitate DNA recognition by providing a trade-off between folding and specific binding

Dynamic protein–DNA recognition: beyond what can be seen ⬇️

Electrostatic versus nonelectrostatic effects in DNA sequence discrimination by divalent ions Mg2+ and Mn2+

Flexibility of prolyl oligopeptidase: molecular dynamics and molecular framework analysis of the potential substrate pathways.

Flexible segments modulate co-folding of dUTPase and nucleocapsid proteins

Functionally and structurally relevant residues of enzymes: are they segregated or overlapping?

Identification of potential glutaminyl cyclase inhibitors from lead-like libraries by in silico and in vitro fragment-based screening

Interfacial water as a "hydration fingerprint" in the noncognate complex of BamHI.

Investigation of protein folding: Uneven distribution of point mutations along polypeptide chains ⬇️

Is there a biological cost of protein disorder? Analysis of cancer-associated mutations

Local structural disorder imparts plasticity on linear motifs.

MFIB: a repository of protein complexes with mutual folding induced by binding.

Macromolecular Interactions of Disordered Proteins

Malleable machines in transcription regulation: the mediator complex

Membrane topology of human ABC proteins.

Metal-binding sites at the active site of restriction endonuclease BamHI can conform to a one-ion mechanism

Molecular Principles of the Interactions of Disordered Proteins

Nucleotide pyrophosphatase employs a P-loop-like motif to enhance catalytic power and NDP/NTP discrimination.

PDBTM: Protein Data Bank of transmembrane proteins after 8 years

PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank

Phosphorylation-induced transient intrinsic structure in the kinase-inducible domain of CREB facilitates its recognition by the KIX domain of CBP

Physical Background of the Disordered Nature of "Mutual Synergetic Folding" Proteins

Possible mechanism for the dynamic stabilization of protein structure ⬇️

Predicting redox state of cysteines in proteins.

Prevalent structural disorder in E. coli and S. cerevisiae proteomes.

Probing the two-metal ion mechanism in the restriction endonuclease BamHI.

Proteins with complex architecture as potential targets for drug design: a case study of Mycobacterium tuberculosis

QM/MM simulation of liquid water with an adaptive quantum region

Rod models of DNA: sequence-dependent anisotropic elastic modelling of local bending phenomena

Role of base flipping in specific recognition of damaged DNA by repair enzymes.

Role of stabilization centers in 4 helix bundle proteins

SCide: identification of stabilization centers in proteins ⬇️

Sequence and Structure Properties Uncover the Natural Classification of Protein Complexes Formed by Intrinsically Disordered Proteins via Mutual Synergistic Folding ⬇️

Sequential, Structural and Functional Properties of Protein Complexes Are Defined by How Folding and Binding Intertwine

Series of concentration-induced phase transitions in cholesterol/phosphatidylcholine mixtures.

Stabilization centers in proteins: identification, characterization and predictions.

Systematic analysis of somatic mutations driving cancer: uncovering functional protein regions in disease development.

TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter.

TOPDB: topology data bank of transmembrane proteins

The BiSearch web server

The energy gap as a universal reaction coordinate for the simulation of chemical reactions

The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins.

The role of DNA bending in Cro protein-DNA interactions ⬇️

The role of dimerization in prion replication

The role of hydrophobic microenvironments in modulating pKa shifts in proteins.

Topology Prediction of Helical Transmembrane Proteins: How Far Have We Reached? ⬇️

Transmembrane proteins in the Protein Data Bank: identification and classification.