Author details

Full Name

PaweÅ¿ Krupa

Affiliation

ORCID

Career Start Year

2013

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37517559	Why does the herpes simplex 1 virus-encoded UL49.5 protein fail to inhibit the TAP-dependent antigen presentation?	Biochim Biophys Acta Biomembr	2023
37628878	Amyloid- Tetramers and Divalent Cations at the Membrane/Water Interface: Simple Models Support a Functional Role.		2023
36646375	The N-terminal Proline Hinge Motif Controls the Structure of Bovine Herpesvirus 1-encoded Inhibitor of the Transporter Associated with Antigen Processing Required for its Immunomodulatory Function.		2023
36795947	Unusual Robustness of Neurotransmitter Vesicle Membranes against Serotonin-Induced Perturbations.		2023
35167070	Computational Models for the Study of Protein Aggregation.	Methods in Molecular Biology	2022
35975925	Mechanical Stability of Ribonuclease A Heavily Depends on the Redox Environment.	Journal of Physical Chemistry B	2022
35580354	Amyloid Î² Dodecamer Disrupts the Neuronal Membrane More Strongly than the Mature Fibril: Understanding the Role of Oligomers in Neurotoxicity.	Journal of Physical Chemistry B	2022
34845623	Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field.	Methods in Molecular Biology	2022
34419932	Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment.	Journal of Molecular Graphics and Modelling	2021
33098838	Plant isoquinoline alkaloids as potential neurodrugs: A comparative study of the effects of benzo[c]phenanthridine and berberine-based compounds on Î²-amyloid aggregation.		2021
33246194	Prediction of CD28-CD86 protein complex structure using different level of resolution approach.	Journal of Molecular Graphics and Modelling	2021
33079977	UNRES-Dock-protein-protein and peptide-protein docking by coarse-grained replica-exchange MD simulations.		2021
32212625	Computational Model to Unravel the Function of Amyloid-Î² Peptides in Contact with a Phospholipid Membrane.	Journal of Physical Chemistry B	2020
32145953	Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers.	Progress in Molecular Biology and Translational Science	2020
31999919	Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13.	J Chem Inf Model	2020
31365254	Structure and Physicochemical Properties of the AÎ²42 Tetramer: Multiscale Molecular Dynamics Simulations.	Journal of Physical Chemistry B	2019
31612567	Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment.	Proteins	2019
31376733	Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment.	Journal of Molecular Graphics and Modelling	2019
29458330	Gait pattern in patients with peripheral artery disease.	BMC Geriatrics	2018
30513992	Reoptimized UNRES Potential for Protein Model Quality Assessment.	Genes	2018
29967418	An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12.	Sci Rep	2018
29860162	Use of the UNRES force field in template-assisted prediction of protein structures and the refinement of server models: Test with CASP12 targets.	J Mol Graph Model	2018
30080414	Computational Studies of the Mechanical Stability for Single-Strand Break DNA.	Journal of Physical Chemistry B	2018
29134679	Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information.	Proteins: Structure, Function and Bioinformatics	2018
29283263	Correction to Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics.	Journal of Chemical Information and Modeling	2018
28194966	What Makes Telomeres Unique?	Journal of Physical Chemistry B	2017
28809487	Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics.	Journal of Chemical Information and Modeling	2017
28942648	Dynamics of Disulfide-Bond Disruption and Formation in the Thermal Unfolding of Ribonuclease A.	Journal of Chemical Theory and Computation	2017
28940211	Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins.	J Comput Chem	2017
28696446	Inhibitors or toxins? Large library target-specific screening of fullerene-based nanoparticles for drug design purpose.	Nanoscale	2017
27615507	Role of the sulfur to Î±-carbon thioether bridges in thurincin H.	Journal of Biomolecular Structure and Dynamics	2017
27749055	Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field.	J Chem Inf Model	2016
27378298	Performance of protein-structure predictions with the physics-based UNRES force field in CASP11.		2016
26483482	Preventing fibril formation of a protein by selective mutation.	Proceedings of the National Academy of Sciences of the United States of America	2015
25691834	Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the UNited RESidue (UNRES) force field for protein simulations.	Journal of Chemical Theory and Computation	2015
25731877	Studies of conformational changes of an arginine-binding protein from Thermotoga maritima in the presence and absence of ligand via molecular dynamics simulations with the coarse-grained UNRES force field.	Journal of Molecular Modeling	2015
25965196	Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field.	J Chem Inf Model	2015
25973573	Molecular modeling of the binding modes of the iron-sulfur protein to the Jac1 co-chaperone from Saccharomyces cerevisiae by all-atom and coarse-grained approaches.	Proteins: Structure, Function and Bioinformatics	2015
25024008	A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions.	Journal of Molecular Modeling	2014
24677212	WeFold: a coopetition for protein structure prediction.	Proteins	2014
23980156	Lessons from application of the UNRES force field to predictions of structures of CASP10 targets.	Proceedings of the National Academy of Sciences of the United States of America	2013
24273465	Improvement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone- and side-chain-local conformational states.	Journal of Chemical Theory and Computation	2013