List of works - Olli T Pentikäinen

2NH and 3OH are crucial structural requirements in sphingomyelin for sticholysin II binding and pore formation in bilayer membranes.

scientific article published on 30 January 2013

A Novel Structural Unit in the N-terminal Region of Filamins

scientific article

A Practical Perspective: The Effect of Ligand Conformers on the Negative Image-Based Screening

scientific article published on 06 June 2019

A dimeric ternary complex of FGFR [correction of FGFR1], heparin and FGF-1 leads to an 'electrostatic sandwich' model for heparin binding

scientific article published in June 1999

A peptide inhibiting the collagen binding function of integrin alpha2I domain.

scientific article

A small-molecule inhibitor of integrin alpha2 beta1 introduces a new strategy for antithrombotic therapy.

scientific article published in December 2009

AMPA receptors and bacterial periplasmic amino acid-binding proteins share the ionic mechanism of ligand recognition

scientific article published on August 1998

Antiferritin VL homodimer binds human spleen ferritin with high specificity

scientific article

BODIL: a molecular modeling environment for structure-function analysis and drug design

scientific article published in June 2004

Binding Properties of HABA-Type Azo Derivatives to Avidin and Avidin-Related Protein 4

scientific article published on 01 October 2006

Blocking oestradiol synthesis pathways with potent and selective coumarin derivatives.

scientific article published in December 2018

Case-specific performance of MM-PBSA, MM-GBSA, and SIE in virtual screening

scientific article published on 30 October 2015

Chicken avidin-related protein 4/5 shows superior thermal stability when compared with avidin while retaining high affinity to biotin.

scientific article

Chicken avidin-related proteins show altered biotin-binding and physico-chemical properties as compared with avidin.

scientific article published on May 2002

Comparison of virtual high-throughput screening methods for the identification of phosphodiesterase-5 inhibitors

scientific article published on 01 June 2011

Construction of hevein (Hev b 6.02) with reduced allergenicity for immunotherapy of latex allergy by comutation of six amino acid residues on the conformational IgE epitopes.

scientific article published in February 2004

Cooperative symmetric to asymmetric conformational transition of the apo-form of scavenger decapping enzyme revealed by simulations

scientific article published on 01 February 2008

Coumarin-Based Profluorescent and Fluorescent Substrates for Determining Xenobiotic-Metabolizing Enzyme Activities In Vitro ⬇️

scientific article published on 01 July 2020

Cyanidin-3-glucoside binds to talin and modulates colon cancer cell adhesions and 3D growth

scientific article published on 09 January 2020

Cystic fibrosis transmembrane conductance regulator interacts with multiple immunoglobulin domains of filamin A.

scientific article

Detection of Binding Sites on SARS-CoV-2 Spike Protein Receptor-Binding Domain by Molecular Dynamics Simulations in Mixed Solvents

scientific article published on 29 April 2021

Determinants of antagonist binding at the alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor subunit, GluR-D. Role of the conserved arginine 507 and glutamate 727 residues

scientific article published in December 2002

Determination of binding site residues responsible for the subunit selectivity of novel marine-derived compounds on kainate receptors

scientific article published on 14 March 2006

Development of New Coumarin-Based Profluorescent Substrates for Human Cytochrome P450 Enzymes

article

Discovery of Retinoic Acid-Related Orphan Receptor γt Inverse Agonists via Docking and Negative Image-Based Screening

scientific article published on 11 June 2018

Discrimination between agonists and antagonists by the alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid-selective glutamate receptor. A mutation analysis of the ligand-binding domain of GluR-D subunit

scientific article published on 7 August 2002

Divergent pharmacological activity of novel marine-derived excitatory amino acids on glutamate receptors

scientific article published on 24 May 2005

Effects of cold acclimation and dsRNA injections on Gs1l gene splicing in Drosophila montana.

scientific article

Efficient virtual screening using multiple protein conformations described as negative images of the ligand-binding site

scientific article

Exploring kainate receptor pharmacology using molecular dynamics simulations.

scientific article

Fluorescent small molecule probe to modulate and explore α2β1 integrin function

scientific article published on 30 August 2011

Fragment- and negative image-based screening of phosphodiesterase 10A inhibitors

scientific article published on 19 July 2019

Full Domain Closure of the Ligand-binding Core of the Ionotropic Glutamate Receptor iGluR5 Induced by the High Affinity Agonist Dysiherbaine and the Functional Antagonist 8,9-Dideoxyneodysiherbaine

scientific article

Full and partial agonism of ionotropic glutamate receptors indicated by molecular dynamics simulations.

scientific article published on 2 May 2011

Functional display of an alpha2 integrin-specific motif (RKK) on the surface of baculovirus particles

scientific article published on August 2005

Getting Docking into Shape Using Negative Image-Based Rescoring

scientific article published on 24 July 2019

Identification of estrogen receptor α ligands with virtual screening techniques.

scientific article published on 4 January 2016

Identification of the Privileged Position in the Imidazo[1,2-a]pyridine Ring of Phosphonocarboxylates for Development of Rab Geranylgeranyl Transferase (RGGT) Inhibitors

scientific article published on 27 September 2017

Improving Docking Performance Using Negative Image-Based Rescoring.

scientific article

In vitro glucuronidation of 7-hydroxycoumarin derivatives in intestine and liver microsomes of Beagle dogs

scientific article published on 25 October 2019

In vitro sulfonation of 7-hydroxycoumarin derivatives in liver cytosol of human and six animal species

scientific article published on 08 January 2020

Inhibition of Pneumolysin Cytotoxicity by Hydrolysable Tannins

scientific article published on 21 December 2020

Inhibition of human CYP1 enzymes by a classical inhibitor α-naphthoflavone and a novel inhibitor N-(3, 5-dichlorophenyl)cyclopropanecarboxamide: An in vitro and in silico study

scientific article published on 14 February 2020

Inhibitory effects and oxidation of 6-methylcoumarin, 7-methylcoumarin and 7-formylcoumarin via human CYP2A6 and its mouse and pig orthologous enzymes

scientific article published on 11 June 2015

Integrin α2I Domain Recognizes Type I and Type IV Collagens by Different Mechanisms

scientific article published in Journal of Biological Chemistry

Jararhagin-derived RKKH peptides induce structural changes in alpha1I domain of human integrin alpha1beta1

scientific article

L-arabinose/D-galactose 1-dehydrogenase of Rhizobium leguminosarum bv. trifolii characterised and applied for bioconversion of L-arabinose to L-arabonate with Saccharomyces cerevisiae

scientific article published on 19 September 2014

Ligand-binding domain determines endoplasmic reticulum exit of AMPA receptors

scientific article published on 13 September 2010

MMGBSA as a tool to understand the binding affinities of filamin-peptide interactions

scientific article

Model structures of the N-methyl-D-aspartate receptor subunit NR1 explain the molecular recognition of agonist and antagonist ligands

scientific article published in March 2004

Modeling of interactions between xenobiotics and cytochrome P450 (CYP) enzymes

scientific article published on 12 June 2015

Molecular Basis of Filamin A-FilGAP Interaction and Its Impairment in Congenital Disorders Associated with Filamin A Mutations

scientific article

Molecular and ecological signs of mitochondrial adaptation: consequences for introgression?

scientific article

Molecular docking and oxidation kinetics of 3-phenyl coumarin derivatives by human CYP2A13

scientific article

Molecular docking-based design and development of a highly selective probe substrate for UDP-glucuronosyltransferase 1A10.

scientific article published on 8 February 2018

Molecular mechanism of T-cell protein tyrosine phosphatase (TCPTP) activation by mitoxantrone

scientific article

New inhibitors of 17beta-hydroxysteroid dehydrogenase type 1.

scientific article published on 18 January 2006

Novel Hydrazine Molecules as Tools To Understand the Flexibility of Vascular Adhesion Protein-1 Ligand-Binding Site: Toward More Selective Inhibitors ⬇️

scientific article published on March 15, 2011

Novel analogs and stereoisomers of the marine toxin neodysiherbaine with specificity for kainate receptors

scientific article

Novel α2β1 integrin inhibitors reveal that integrin binding to collagen under shear stress conditions does not require receptor preactivation.

scientific article

Pharmacological activity of C10-substituted analogs of the high-affinity kainate receptor agonist dysiherbaine.

scientific article

Pro-prion binds filamin A, facilitating its interaction with integrin beta1, and contributes to melanomagenesis

scientific article

Reliability of Virtual Screening Methods in Prediction of PDE4B-inhibitor Activity.

scientific article published on 02 July 2015

Rocker: Open source, easy-to-use tool for AUC and enrichment calculations and ROC visualization

scientific article (publication date: 2016)

Screening of Natural Products Targeting SARS-CoV-2-ACE2 Receptor Interface - A MixMD Based HTVS Pipeline

scientific article published on 19 November 2020

Selective agonist binding of (S)-2-amino-3-(3-hydroxy-5-methyl-4-isoxazolyl)propionic acid (AMPA) and 2S-(2alpha,3beta,4beta)-2-carboxy-4-(1-methylethenyl)-3-pyrrolidineacetic acid (kainate) receptors: a molecular modeling study

scientific article published in December 2003

Skeletal Dysplasia Mutations Effect on Human Filamins' Structure and Mechanosensing

scientific article

Small molecule designed to target metal binding site in the alpha2I domain inhibits integrin function.

scientific article published on 21 April 2007

Structural mechanism of N-methyl-D-aspartate receptor type 1 partial agonism

scientific article

Structure of three tandem filamin domains reveals auto-inhibition of ligand binding

scientific article

Structure-Activity Relationship Analysis of 3-Phenylcoumarin-Based Monoamine Oxidase B Inhibitors.

scientific article published on 2 March 2018

Structure-activity relationship of sphingomyelin analogs with sphingomyelinase from Bacillus cereus

scientific article

Substrate Selectivity of Coumarin Derivatives by Human CYP1 Enzymes: In Vitro Enzyme Kinetics and In Silico Modeling

scientific article

Subtype selectivity and flexibility of ionotropic glutamate receptors upon antagonist ligand binding

scientific article published on 26 January 2006

Suitability of MMGBSA for the selection of correct ligand binding modes from docking results

scientific article published on 23 December 2018

Synthesis and pharmacological characterization of N3-substituted willardiine derivatives: role of the substituent at the 5-position of the uracil ring in the development of highly potent and selective GLUK5 kainate receptor antagonists

scientific article

Synthesis, in Vitro Activity, and Three-Dimensional Quantitative Structure−Activity Relationship of Novel Hydrazine Inhibitors of Human Vascular Adhesion Protein-1 ⬇️

scientific article published on September 9, 2010

Temperature-dependent mutational robustness can explain faster molecular evolution at warm temperatures, affecting speciation rate and global patterns of species diversity

scientific article published in 2015

The Influence of Hydrogen Bonding on Sphingomyelin/Colipid Interactions in Bilayer Membranes

scientific article published on January 2016

The core domain of retrotransposon integrase in Hordeum: predicted structure and evolution.

scientific article published in September 1998

The major conformational IgE-binding epitopes of hevein (Hev b6.02) are identified by a novel chimera-based allergen epitope mapping strategy.

scientific article

Ultrafast protein structure-based virtual screening with Panther.

scientific article

Vascular amine oxidases are needed for leukocyte extravasation into inflamed joints in vivo

scientific article published on 01 September 2006

alpha 11beta 1 integrin recognizes the GFOGER sequence in interstitial collagens

scientific article

“RKKH” Peptides from the Snake Venom Metalloproteinase ofBothrops jararacaBind Near the Metal Ion-dependent Adhesion Site of the Human Integrin α2I-domain

scientific article published in Journal of Biological Chemistry

List of works by Olli T Pentikäinen

2NH and 3OH are crucial structural requirements in sphingomyelin for sticholysin II binding and pore formation in bilayer membranes.

A Novel Structural Unit in the N-terminal Region of Filamins

A Practical Perspective: The Effect of Ligand Conformers on the Negative Image-Based Screening

A dimeric ternary complex of FGFR [correction of FGFR1], heparin and FGF-1 leads to an 'electrostatic sandwich' model for heparin binding

A peptide inhibiting the collagen binding function of integrin alpha2I domain.

A small-molecule inhibitor of integrin alpha2 beta1 introduces a new strategy for antithrombotic therapy.

AMPA receptors and bacterial periplasmic amino acid-binding proteins share the ionic mechanism of ligand recognition

Antiferritin VL homodimer binds human spleen ferritin with high specificity

BODIL: a molecular modeling environment for structure-function analysis and drug design

Binding Properties of HABA-Type Azo Derivatives to Avidin and Avidin-Related Protein 4

Blocking oestradiol synthesis pathways with potent and selective coumarin derivatives.

Case-specific performance of MM-PBSA, MM-GBSA, and SIE in virtual screening

Chicken avidin-related protein 4/5 shows superior thermal stability when compared with avidin while retaining high affinity to biotin.

Chicken avidin-related proteins show altered biotin-binding and physico-chemical properties as compared with avidin.

Comparison of virtual high-throughput screening methods for the identification of phosphodiesterase-5 inhibitors

Construction of hevein (Hev b 6.02) with reduced allergenicity for immunotherapy of latex allergy by comutation of six amino acid residues on the conformational IgE epitopes.

Cooperative symmetric to asymmetric conformational transition of the apo-form of scavenger decapping enzyme revealed by simulations

Coumarin-Based Profluorescent and Fluorescent Substrates for Determining Xenobiotic-Metabolizing Enzyme Activities In Vitro ⬇️

Cyanidin-3-glucoside binds to talin and modulates colon cancer cell adhesions and 3D growth

Cystic fibrosis transmembrane conductance regulator interacts with multiple immunoglobulin domains of filamin A.

Detection of Binding Sites on SARS-CoV-2 Spike Protein Receptor-Binding Domain by Molecular Dynamics Simulations in Mixed Solvents

Determinants of antagonist binding at the alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor subunit, GluR-D. Role of the conserved arginine 507 and glutamate 727 residues

Determination of binding site residues responsible for the subunit selectivity of novel marine-derived compounds on kainate receptors

Development of New Coumarin-Based Profluorescent Substrates for Human Cytochrome P450 Enzymes

Discovery of Retinoic Acid-Related Orphan Receptor γt Inverse Agonists via Docking and Negative Image-Based Screening

Discrimination between agonists and antagonists by the alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid-selective glutamate receptor. A mutation analysis of the ligand-binding domain of GluR-D subunit

Divergent pharmacological activity of novel marine-derived excitatory amino acids on glutamate receptors

Effects of cold acclimation and dsRNA injections on Gs1l gene splicing in Drosophila montana.

Efficient virtual screening using multiple protein conformations described as negative images of the ligand-binding site

Exploring kainate receptor pharmacology using molecular dynamics simulations.

Fluorescent small molecule probe to modulate and explore α2β1 integrin function

Fragment- and negative image-based screening of phosphodiesterase 10A inhibitors

Full Domain Closure of the Ligand-binding Core of the Ionotropic Glutamate Receptor iGluR5 Induced by the High Affinity Agonist Dysiherbaine and the Functional Antagonist 8,9-Dideoxyneodysiherbaine

Full and partial agonism of ionotropic glutamate receptors indicated by molecular dynamics simulations.

Functional display of an alpha2 integrin-specific motif (RKK) on the surface of baculovirus particles

Getting Docking into Shape Using Negative Image-Based Rescoring

Identification of estrogen receptor α ligands with virtual screening techniques.

Identification of the Privileged Position in the Imidazo[1,2-a]pyridine Ring of Phosphonocarboxylates for Development of Rab Geranylgeranyl Transferase (RGGT) Inhibitors

Improving Docking Performance Using Negative Image-Based Rescoring.

In vitro glucuronidation of 7-hydroxycoumarin derivatives in intestine and liver microsomes of Beagle dogs

In vitro sulfonation of 7-hydroxycoumarin derivatives in liver cytosol of human and six animal species

Inhibition of Pneumolysin Cytotoxicity by Hydrolysable Tannins

Inhibition of human CYP1 enzymes by a classical inhibitor α-naphthoflavone and a novel inhibitor N-(3, 5-dichlorophenyl)cyclopropanecarboxamide: An in vitro and in silico study

Inhibitory effects and oxidation of 6-methylcoumarin, 7-methylcoumarin and 7-formylcoumarin via human CYP2A6 and its mouse and pig orthologous enzymes

Integrin α2I Domain Recognizes Type I and Type IV Collagens by Different Mechanisms

Jararhagin-derived RKKH peptides induce structural changes in alpha1I domain of human integrin alpha1beta1

L-arabinose/D-galactose 1-dehydrogenase of Rhizobium leguminosarum bv. trifolii characterised and applied for bioconversion of L-arabinose to L-arabonate with Saccharomyces cerevisiae

Ligand-binding domain determines endoplasmic reticulum exit of AMPA receptors

MMGBSA as a tool to understand the binding affinities of filamin-peptide interactions

Model structures of the N-methyl-D-aspartate receptor subunit NR1 explain the molecular recognition of agonist and antagonist ligands

Modeling of interactions between xenobiotics and cytochrome P450 (CYP) enzymes

Molecular Basis of Filamin A-FilGAP Interaction and Its Impairment in Congenital Disorders Associated with Filamin A Mutations

Molecular and ecological signs of mitochondrial adaptation: consequences for introgression?

Molecular docking and oxidation kinetics of 3-phenyl coumarin derivatives by human CYP2A13

Molecular docking-based design and development of a highly selective probe substrate for UDP-glucuronosyltransferase 1A10.

Molecular mechanism of T-cell protein tyrosine phosphatase (TCPTP) activation by mitoxantrone

New inhibitors of 17beta-hydroxysteroid dehydrogenase type 1.

Novel Hydrazine Molecules as Tools To Understand the Flexibility of Vascular Adhesion Protein-1 Ligand-Binding Site: Toward More Selective Inhibitors ⬇️

Novel analogs and stereoisomers of the marine toxin neodysiherbaine with specificity for kainate receptors

Novel α2β1 integrin inhibitors reveal that integrin binding to collagen under shear stress conditions does not require receptor preactivation.

Pharmacological activity of C10-substituted analogs of the high-affinity kainate receptor agonist dysiherbaine.

Pro-prion binds filamin A, facilitating its interaction with integrin beta1, and contributes to melanomagenesis

Reliability of Virtual Screening Methods in Prediction of PDE4B-inhibitor Activity.

Rocker: Open source, easy-to-use tool for AUC and enrichment calculations and ROC visualization

Screening of Natural Products Targeting SARS-CoV-2-ACE2 Receptor Interface - A MixMD Based HTVS Pipeline

Selective agonist binding of (S)-2-amino-3-(3-hydroxy-5-methyl-4-isoxazolyl)propionic acid (AMPA) and 2S-(2alpha,3beta,4beta)-2-carboxy-4-(1-methylethenyl)-3-pyrrolidineacetic acid (kainate) receptors: a molecular modeling study

Skeletal Dysplasia Mutations Effect on Human Filamins' Structure and Mechanosensing

Small molecule designed to target metal binding site in the alpha2I domain inhibits integrin function.

Structural mechanism of N-methyl-D-aspartate receptor type 1 partial agonism

Structure of three tandem filamin domains reveals auto-inhibition of ligand binding

Structure-Activity Relationship Analysis of 3-Phenylcoumarin-Based Monoamine Oxidase B Inhibitors.

Structure-activity relationship of sphingomyelin analogs with sphingomyelinase from Bacillus cereus

Substrate Selectivity of Coumarin Derivatives by Human CYP1 Enzymes: In Vitro Enzyme Kinetics and In Silico Modeling

Subtype selectivity and flexibility of ionotropic glutamate receptors upon antagonist ligand binding

Suitability of MMGBSA for the selection of correct ligand binding modes from docking results

Synthesis and pharmacological characterization of N3-substituted willardiine derivatives: role of the substituent at the 5-position of the uracil ring in the development of highly potent and selective GLUK5 kainate receptor antagonists

Synthesis, in Vitro Activity, and Three-Dimensional Quantitative Structure−Activity Relationship of Novel Hydrazine Inhibitors of Human Vascular Adhesion Protein-1 ⬇️

Temperature-dependent mutational robustness can explain faster molecular evolution at warm temperatures, affecting speciation rate and global patterns of species diversity

The Influence of Hydrogen Bonding on Sphingomyelin/Colipid Interactions in Bilayer Membranes