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List of works by Jiří Vondrášek

A community proposal to integrate proteomics activities in ELIXIR

scientific article

A comparison of approaches to accessing existing biological and chemical relational databases via SPARQL

scientific article published in 2023

AMBER and CHARMM Force Fields Inconsistently Portray the Microscopic Details of Phosphorylation

scientific article published on 06 December 2018

Activation route of the Schistosoma mansoni cathepsin B1 drug target: structural map with a glycosaminoglycan switch

scientific article

Advanced SPARQL querying in small molecule databases

scientific article (publication date: 2016)

Ameloblastin Peptides Modulates the Osteogenic Capacity of Human Mesenchymal Stem Cells

scientific article published on 7 February 2017

An ameloblastin C-terminus variant is present in human adipose tissue

An intrinsically disordered proteins community for ELIXIR

scientific article published on 15 October 2019

Analysis of energy stabilization inside the hydrophobic core of rubredoxin.

scientific article

Another role of proline: stabilization interactions in proteins and protein complexes concerning proline and tryptophane.

scientific article

Application of InChI to curate, index, and query 3-D structures

scientific article (publication date: 28 April 2005)

Artificial proteins as allosteric modulators of PDZ3 and SH3 in two-domain constructs: A computational characterization of novel chimeric proteins

scientific article published on 6 June 2016

Bioinformatic analysis and molecular modelling of human ameloblastin suggest a two-domain intrinsically unstructured calcium-binding protein

scientific article published in April 2008

Biophysical characterization of recombinant human ameloblastin

scientific article published on 01 December 2011

Can All-Atom Molecular Dynamics Simulations Quantitatively Describe Homeodomain-DNA Binding Equilibria?

scientific article published on 12 March 2019

Cathepsin D Propeptide: Mechanism and Regulation of Its Interaction with the Catalytic Core†

scientific article published on 01 December 2006

Characterization of AMBN I and II Isoforms and Study of Their Ca<sup>2+</sup>-Binding Properties

scientific article published on 05 December 2020

Characterization of the part of N-terminal PIP2 binding site of the TRPM1 channel.

scientific article published on 27 October 2015

Chemical compound navigator: a web-based chem-BLAST, chemical taxonomy-based search engine for browsing compounds

scientific article published on June 2006

Computational methods for the description of pharmacologically relevant platinum complexes – molecular structure and bond dissociation

scholarly article by Malte Kokoschka et al published 2016 in Physical Chemistry Chemical Physics

Correction to: Interoperable chemical structure search service

publication published on 13 February 2020

Critical Assessment of Current Force Fields. Short Peptide Test Case

scientific article published on 14 December 2012

Dispersion Interactions Govern the Strong Thermal Stability of a Protein

scientific article published on 01 January 2007

Effect of TFE on the Helical Content of AK17 and HAL-1 Peptides: Theoretical Insights into the Mechanism of Helix Stabilization

scientific article published on 03 February 2016

Effect of enamel matrix derivative and of proline-rich synthetic peptides on the differentiation of human mesenchymal stem cells toward the osteogenic lineage

scientific article

Efficient Estimation of Absolute Binding Free Energy for a Homeodomain-DNA Complex from Nonequilibrium Pulling Simulations

scientific article published on 27 March 2020

Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins

scientific article published on July 2010

Exquisite ligand stereoselectivity of a Drosophila juvenile hormone receptor contrasts with its broad agonist repertoire

scientific article published on 19 November 2018

Free-thiol Cys331 exposed during activation process is critical for native tetramer structure of cathepsin C (dipeptidyl peptidase I).

scientific article published on April 2002

Generalized EmbedSOM on quadtree-structured self-organizing maps

scientific article published on 18 December 2019

GigaSOM.jl: High-performance clustering and visualization of huge cytometry datasets

scientific article published on 01 November 2020

GigaSOM.jl: High-performance clustering and visualization of huge cytometry datasets

scientific article published on 4 August 2020

Gyration- and inertia-tensor-based collective coordinates for metadynamics. Application on the conformational behavior of polyalanine peptides and Trp-cage folding

scientific article published on 30 September 2011

HIVdb: a database of the structures of human immunodeficiency virus protease

scientific article published in December 2002

Homology modeling and SAR analysis of Schistosoma japonicum cathepsin D (SjCD) with statin inhibitors identify a unique active site steric barrier with potential for the design of specific inhibitors.

scientific article published in April 2005

How to fragment a polypeptide? An ab initio computational study of pair interactions between amino acids and ligand-amino acids in proteins

scientific article published in 2011

Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation

scientific article published on 02 June 2020

Hypertrophic cardiomyopathy: from mutation to functional analysis of defective protein ⬇️

scientific article published on June 1, 2011

IDSM ChemWebRDF: SPARQLing small-molecule datasets

scientific article

Identifying stabilizing key residues in proteins using interresidue interaction energy matrix.

scientific article

Increasing affinity of interferon-γ receptor 1 to interferon-γ by computer-aided design.

scientific article published on 2 October 2013

Insights into Unfolded Proteins from the Intrinsic ϕ/ψ Propensities of the AAXAA Host-Guest Series

scientific article published in January 2016

Interoperable chemical structure search service

scientific article published on 28 June 2019

Intrinsically disordered enamel matrix protein ameloblastin forms ribbon-like supramolecular structures via an N-terminal segment encoded by exon 5

scientific article published on 19 June 2013

Intrinsically disordered protein domain of human ameloblastin in synthetic fusion with calmodulin increases calmodulin stability and modulates its function

scientific article published on 05 December 2020

Ion specific effects of sodium and potassium on the catalytic activity of HIV-1 protease

article

Large-Scale Quantitative Assessment of Binding Preferences in Protein-Nucleic Acid Complexes.

scientific article published in April 2015

Loss of dispersion energy changes the stability and folding/unfolding equilibrium of the Trp-cage protein.

scientific article

Mapping of CaM, S100A1 and PIP2-Binding Epitopes in the Intracellular N- and C-Termini of TRPM4

scientific article published on 17 June 2020

MedusaScore: an accurate force field-based scoring function for virtual drug screening

scientific article published on 02 August 2008

Metadynamics as a tool for mapping the conformational and free-energy space of peptides--the alanine dipeptide case study.

scientific article

Model of peptide bond-aromatic ring interaction: correlated ab initio quantum chemical study

scientific article published on 2 August 2007

Noncovalent Interactions in Specific Recognition Motifs of Protein-DNA Complexes

scientific article published on 19 December 2016

Novel Structural Mechanism of Allosteric Regulation of Aspartic Peptidases via an Evolutionarily Conserved Exosite

scientific article published on 26 January 2018

Novel high-affinity binders of human interferon gamma derived from albumin-binding domain of protein G.

scientific article

On InChI and evaluating the quality of cross-reference links

scientific article (publication date: 2014)

PIP2 and PIP3 interact with N-terminus region of TRPM4 channel

scientific article

Parametrization of 2,2,2-trifluoroethanol based on the generalized AMBER force field provides realistic agreement between experimental and calculated properties of pure liquid as well as water-mixed solutions

scientific article published on 25 August 2014

Phosphorylation Modulates Ameloblastin Self-assembly and Ca 2+ Binding

scientific article published on 27 July 2017

Prolyl Oligopeptidase from the Blood Fluke Schistosoma mansoni: From Functional Analysis to Anti-schistosomal Inhibitors

scientific article

Quantification and rationalization of the higher affinity of sodium over potassium to protein surfaces

scholarly article

Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples

scholarly article by Jan Řezáč et al published 2008 in Collection of Czechoslovak Chemical Communications

Random protein sequences can form defined secondary structures and are well-tolerated in vivo.

scientific article published on 13 November 2017

Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures

scientific article published on April 2009

Representative Amino Acid Side-Chain Interactions in Protein-DNA Complexes: A Comparison of Highly Accurate Correlated Ab Initio Quantum Mechanical Calculations and Efficient Approaches for Applications to Large Systems

scientific article published on 6 August 2015

Retro operation on the Trp-cage miniprotein sequence produces an unstructured molecule capable of folding similar to the original only upon 2,2,2-trifluoroethanol addition.

scientific article

Rigid duplex alpha-cyclodextrin reversibly connected with disulfide bonds. Synthesis and inclusion complexes.

scientific article

Sachem: a chemical cartridge for high-performance substructure search.

scientific article

Sequence Versus Composition: What Prescribes IDP Biophysical Properties?

scientific article published on 03 July 2019

Sequence-Specific Recognition of DNA by Proteins: Binding Motifs Discovered Using a Novel Statistical/Computational Analysis

scientific article

Shared CaM- and S100A1-binding epitopes in the distal TRPM4 N terminus

scientific article

ShinySOM: Graphical SOM-based analysis of single-cell cytometry data

scientific article published on 12 February 2020

SmSP2: A serine protease secreted by the blood fluke pathogen Schistosoma mansoni with anti-hemostatic properties

scientific article published on 20 April 2018

TRPM6 N-Terminal CaM- and S100A1-Binding Domains

scientific article published on 09 September 2019

The IDSM mass spectrometry extension: searching mass spectra using SPARQL

scientific article published on 29 March 2024

The LOTUS Initiative for Open Natural Products Research: Knowledge Management through Wikidata

scholarly article (preprint) by Adriano Rutz published in March 2021

The LOTUS initiative for open knowledge management in natural products research ⬇️

scholarly article by Adriano Rutz et al. published in May 2022

The Stabilization Energy of the GLU-LYS Salt Bridge in the Protein/Water Environment: Correlated Quantum Chemical ab initio, DFT and Empirical Potential Studies

The bio.tools registry of software tools and data resources for the life sciences

article

The characterization of a novel S100A1 binding site in the N-terminus of TRPM1.

scientific article published on 16 July 2016

The identification of new substrates of human DHRS7 by molecular modeling and in vitro testing.

scientific article published on 4 July 2017

The molecular origin of like-charge arginine-arginine pairing in water

scientific article

Thermodynamic penalty arising from burial of a ligand polar group within a hydrophobic pocket of a protein receptor.

scientific article published in August 2006

Toward Ab Initio Protein Folding: Inherent Secondary Structure Propensity of Short Peptides from the Bioinformatics and Quantum-Chemical Perspective

scientific article published on 31 January 2019

Towards a better understanding of the specificity of protein-protein interaction

scientific article published in November 2012

Trypsin- and Chymotrypsin-like serine proteases in schistosoma mansoni-- 'the undiscovered country'.

scientific article

Unexpectedly Strong Energy Stabilization Inside the Hydrophobic Core of Small Protein Rubredoxin Mediated by Aromatic Residues: Correlated Ab Initio Quantum Chemical Calculations [J. Amer. Chem. Soc.2005,127, 2615−2617]

scientific article published in 2005

Unexpectedly strong energy stabilization inside the hydrophobic core of small protein rubredoxin mediated by aromatic residues: correlated ab initio quantum chemical calculations

scientific article

Unusual binding mode of an HIV-1 protease inhibitor explains its potency against multi-drug-resistant virus strains

scientific article

Urea and Guanidinium Induced Denaturation of a Trp-Cage Miniprotein

scientific article published on 02 June 2011

Widespread evolutionary crosstalk among protein domains in the context of multi-domain proteins

scientific article published in PLoS ONE

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