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List of works by Ivaylo Ivanov

A new structural framework for integrating replication protein A into DNA processing machinery.

scientific article

Ab initio calculations of intramolecular parameters for a class of arylamide polymers

scientific article published on 01 April 2006

Alkylpurine glycosylase D employs DNA sculpting as a strategy to extrude and excise damaged bases

scientific article

Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations.

scientific article

Conserved Structural Chemistry for Incision Activity in Structurally Non-homologous Apurinic/Apyrimidinic Endonuclease APE1 and Endonuclease IV DNA Repair Enzymes

scientific article

Diamidine compounds for selective inhibition of protein arginine methyltransferase 1.

scientific article published on 06 March 2014

Discovery of Decamidine as a New and Potent PRMT1 Inhibitor

scientific article published on 3 January 2017

Distal substitutions drive divergent DNA specificity among paralogous transcription factors through subdivision of conformational space.

scientific article

Dynamical flexibility and proton transfer in the arginase active site probed by ab initio molecular dynamics

scientific article published on 01 March 2005

Envisioning how the prototypic molecular machine TFIIH functions in transcription initiation and DNA repair

scientific article published on 17 September 2020

Enzyme cofactors: double-edged sword for catalysis

scientific article published on 01 January 2013

First-principles study of aqueous hydroxide solutions.

scientific article

Functional dynamics in replication protein A DNA binding and protein recruitment domains

scientific article published on 21 May 2015

Histone H4 Acetylation Differentially Modulates Arginine Methylation by an in Cis Mechanism ⬇️

scientific article published on April 18, 2011

Hydrogen bonding in water

scientific article published on 20 November 2003

Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution

scientific article

Natural Product Micheliolide (MCL) Irreversibly Activates Pyruvate Kinase M2 and Suppresses Leukemia

scientific article published on 11 April 2018

New insights into the GABA(A) receptor structure and orthosteric ligand binding: receptor modeling guided by experimental data. ⬇️

scientific article

Opening pathways of the DNA clamps proliferating cell nuclear antigen and Rad9-Rad1-Hus1.

scientific article published on 12 September 2013

Polymerization and editing modes of a high-fidelity DNA polymerase are linked by a well-defined path

scientific article published on 23 October 2020

Probing DNA clamps with single-molecule force spectroscopy.

scientific article

Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications.

scientific article

Rational design of a protein that binds integrin αvβ3 outside the ligand binding site

scientific article published on 31 May 2016

Recognition of a Key Anchor Residue by a Conserved Hydrophobic Pocket Ensures Subunit Interface Integrity in DNA Clamps

scientific article published on 30 April 2019

Recognition of the ring-opened state of proliferating cell nuclear antigen by replication factor C promotes eukaryotic clamp-loading.

scientific article

Relative pKa values from first-principles molecular dynamics: the case of histidine deprotonation

scientific article published in March 2006

Repair complexes of FEN1 endonuclease, DNA, and Rad9-Hus1-Rad1 are distinguished from their PCNA counterparts by functionally important stability

scientific article

Secondary Interaction Interfaces with PCNA Control Conformational Switching of DNA Polymerase PolB from Polymerization to Editing.

scientific article

Simulation-Based Methods for Model Building and Refinement in Cryoelectron Microscopy

scientific article published on 31 March 2020

Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1.

scientific article published on 23 February 2017

Small molecule binders recognize DNA microstructural variations via an induced fit mechanism

scientific article published on 01 January 2019

Solution X-ray scattering combined with computational modeling reveals multiple conformations of covalently bound ubiquitin on PCNA

scientific article

Structural mechanism of ATP-independent transcription initiation by RNA polymerase I

scientific article

Structural mechanism of helicase loading onto replication origin DNA by ORC-Cdc6

scientific article published on 15 July 2020

Structural visualization of RNA polymerase III transcription machineries

scientific article published on 31 July 2018

Synthetic mimics of antimicrobial peptides.

scientific article published on January 2008

Transcription preinitiation complex structure and dynamics provide insight into genetic diseases

scientific article published on 20 May 2019

Transmembrane peptide-induced lipid sorting and mechanism of Lalpha-to-inverted phase transition using coarse-grain molecular dynamics.

scientific article

Uncovering universal rules governing the selectivity of the archetypal DNA glycosylase TDG.

scientific article published on 21 May 2018

Unexpected Allosteric Network Contributes to LRH-1 Co-regulator Selectivity.

scientific article

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