B. Lesyng

发表

Quantum-dynamical picture of a multistep enzymatic process: reaction catalyzed by phospholipase A(2).

J. Mccammon, P. Bała, P. Grochowski, 2000, Biophysical journal.

Quantum dynamics of proton transfer processes in enzymatic reactions. simulations of phospholipase A2

J. Mccammon, P. Bała, P. Grochowski, 1998 .

Quantum-Classical Molecular Dynamics. Models and Applications

J. Mccammon, P. Bała, P. Grochowski, 1996 .

Density functional based parametrization of a valence bond method and its applications in quantum‐classical molecular dynamics simulations of enzymatic reactions

J. Mccammon, P. Bała, P. Grochowski, 1996 .

AB Initio Studies and Quantum-Classical Molecular Dynamics Simulations for Proton Transfer Processes in Model Systems and in Enzymes

J. Mccammon, P. Bała, T. Truong, 1992 .

Implementation of a symplectic multiple-time-step molecular dynamics algorithm, based on the united-residue mesoscopic potential energy function.

A. Liwo, H. Scheraga, F. Rakowski, 2006, The Journal of chemical physics.

Estimation of Posturographic Trajectory Using k-Nearest Neighbors Classifier in Patients with Rheumatoid Arthritis and Osteoarthritis.

B. Sokołowska, B. Lesyng, T. Sadura-Sieklucka, 2018, Advances in experimental medicine and biology.

A Mezoscopic Model of Nucleic Acids. Part 2. An Effective Potential Energy Function for DNA

M. Maciejczyk, B. Lesyng, W. Rudnicki, 2000, Journal of biomolecular structure & dynamics.

Molecular Mechanics and Dynamics Modeling: Furanose Rings Puckering into DNA and RNA Double Helices

B. Lesyng, W. Rudnicki, V. Pechenaya, 1995 .

Why isoguanine and isocytosine are not the components of the genetic code

B. Lesyng, A. Jaworski, J. S. Kwiatkowski, 2009 .

Tautomerism of pyrimidine bases—uracil, cytosine, isocytosine: Theoretical study with complete optimization of geometry

A. Pohorille, R. Czerminski, B. Lesyng, 1979 .

Effect of water on the tautomeric equilibrium of 2‐oxopyridine. A Monte Carlo simulation study

V. Danilov, B. Lesyng, V. Poltev, 1981 .

Functional connectivity in Alzheimer’s disease and Mild Cognitive Impairment: an EEG study in the framework of DECIDE project

C. Babiloni, R. Lizio, F. Vecchio, 2012 .

Efficacy of 2-halogen substituted d-glucose analogs in blocking glycolysis and killing “hypoxic tumor cells”

K. Ginalski, Johnathan C. Maher, M. Kurtoğlu, 2006, Cancer Chemotherapy and Pharmacology.

Molecular Modeling in Drug Design

B. Lesyng, W. Rudnicki, 2003 .

Inferring Molecular Processes Heterogeneity from Transcriptional Data

Weronika Wronowska, A. Gambin, B. Lesyng, 2017, BioMed research international.

Applications of quantum-classical and quantum-stochastic molecular dynamics simulations for proton transfer processes

James Andrew McCammon, Bogdan Lesyng, Piotr Bała, 1994 .

Surface markers of cancer stem-like cells of ovarian cancer and their clinical relevance

C. Kieda, A. Czarnecka, C. Szczylik, 2018, Contemporary oncology.

Ab initio study of proton transfer in [H3N−H−NH3]+ and [H3N−H−OH2]+

J. Andrew McCammon, Bogdan Lesyng, Lukasz Jaroszewski, 1990 .

The crystal structures of 2'-deoxy-2'-fluorocytidine and 2'-deoxy-2'-fluorouridine

W. Saenger, C. Marck, B. Lesyng, 1982 .

Synthesis, structural and antimicrobial studies of type II topoisomerase-targeted copper(II) complexes of 1,3-disubstituted thiourea ligands.

Sebastian Kmiecik, B. Lesyng, M. Koliński, 2018, Journal of inorganic biochemistry.

Modified π‐SCF MO CI calculations for anionic forms of pyrimidinic nucleic acid bases

B. Lesyng, J. S. Kwiatkowski, 2009 .

Dipole moments of 2,4-diketopyrimidines. II. Uracil, thymine and their derivatives.

M. Geller, B. Lesyng, K. Wierzchowski, 1974, Biochimica et biophysica acta.

Energy minimization and molecular dynamics studies of Asn-102 elastase

Bogdan Lesyng, Edgar F. Meyer, E. Meyer, 1987, J. Comput. Aided Mol. Des..

Vibrations and hydrogen bonding in porphycene.

Mark R. Johnson, B. Lesyng, A. Vdovin, 2012, Physical chemistry chemical physics : PCCP.

The Barrier to Pseudorotation of Furanose Rings and its Biological Implications

B. Lesyng, 1987 .

Ab initio calculations on the barrier to pseudorotation of model 2′‐deoxyfuranose and 2′‐deoxy‐2′‐fluorofuranose rings

C. Marck, B. Lesyng, W. Guschlbauer, 1985 .

Influence of the orientation of hydroxyl groups on the puckering modes of furanoid rings

W. Saenger, B. Lesyng, 1984 .

Barrier to rotation and conformation of the NB2 group in cytosine and its derivatives. Part I. Theoretical study of cytosine.

M. Geller, B. Lesyng, B Lesyng, 1975, Biochimica et biophysica acta.

From experimental, structural probability distributions to the theoretical causality analysis of molecular changes

Franciszek Rakowski, Maciej Dziubiński, Pawel Daniluk, 2012 .

Novel small molecular inhibitors disrupt the JAK/STAT3 and FAK signaling pathways and exhibit a potent antitumor activity in glioma cells

Bozena Kaminska, Jakub Mieczkowski, Bogdan Lesyng, 2012, Cancer biology & therapy.

Theoretical and Computational Aspects of Protein Structural Alignment

Bogdan Lesyng, Pawel Daniluk, B. Lesyng, 2018, Springer Series on Bio- and Neurosystems.

Exploring Covalent Docking Mechanisms of Boron-Based Inhibitors to Class A, C and D β-Lactamases Using Time-dependent Hybrid QM/MM Simulations

Łukasz Charzewski, B. Lesyng, K. Krzyśko, 2021, Frontiers in Molecular Biosciences.

P 11 Pyridine caffeic acid benzyl ester ( CABE ) analogues target the ATP pocket of atypical RIO kinases

W. Zagórski, K. Grzelak, W. Priebe, 2012 .

A genistein derivative, ITB-301, induces microtubule depolymerization and mitotic arrest in multidrug-resistant ovarian cancer

R. Bast, A. Ahmed, X. Le, 2011, Cancer Chemotherapy and Pharmacology.

Prediction of pKas of Titratable Residues in Proteins Using a Poisson-Boltzmann Model of the Solute-Solvent System

J. Andrew McCammon, James M. Briggs, Jan M. Antosiewicz, 1999, Computational Molecular Dynamics.

Modelling of active forms of protein kinases: p38--a case study.

J. Sowadski, K. Ginalski, B. Lesyng, 1997, Acta biochimica Polonica.

Development of novel molecular probes of the Rio1 atypical protein kinase.

W. Zagórski, K. Grzelak, W. Priebe, 2013, Biochimica et biophysica acta.

ResiCon: a method for the identification of dynamic domains, hinges and interfacial regions in proteins

Bogdan Lesyng, Pawel Daniluk, Maciej Dziubinski, 2015, Bioinform..

A novel method to compare protein structures using local descriptors

Bogdan Lesyng, Pawel Daniluk, B. Lesyng, 2011, BMC Bioinformatics.

Tautomerism of oxopyridines and oxopyrimidines: Theoretical study with complete optimization of geometry

A. Pohorille, R. Czerminski, B. Lesyng, 1979 .

A simple model for predicting the free energy of binding between anthracycline antibiotics and DNA.

W. Priebe, B. Lesyng, W. Rudnicki, 2000, Acta biochimica Polonica.

Activities of topoisomerase I in its complex with SRSF1.

A. Girstun, B. Lesyng, K. Starón, 2012, Biochemistry.

Structural characterisation of inhibitory and non-inhibitory MMP-9–TIMP-1 complexes and implications for regulatory mechanisms of MMP-9

Łukasz Charzewski, B. Lesyng, K. Krzyśko, 2021, Scientific Reports.

Analogs of cinnamic acid benzyl amide as nonclassical inhibitors of activated JAK2 kinase.

K. Grzelak, W. Priebe, B. Lesyng, 2014, Current cancer drug targets.

RRM proteins interacting with the cap region of topoisomerase I.

M. Murawska, A. Girstun, B. Lesyng, 2007, Journal of molecular biology.

Parallelization of the quantum dynamics code for cluster architecture and its applications to the Gross-Pitaevskii equation

P. Bała, B. Lesyng, A. Górecki, 2006 .

DFT calculations and parameterization of the approximate valence bond method to describe the phosphoryl transfer reaction in a model system

K. Ginalski, P. Grochowski, B. Lesyng, 2002 .

Modelling of insulin receptor tyrosine kinase in its active form: a case study for validation of theoretical methods.

K. Ginalski, B. Lesyng, M. Wojciechowski, 1999, Acta biochimica Polonica.

AB INITIO AND SEMIEMPIRICAL MOLECULAR ORBITAL STUDIES ON CYTOSINE AND N( 4)HYDROXYCYTOSINE

B. Lesyng, M. Palmer, J. S. Kwiatkowski, 1983 .

A comparative study of time dependent quantum mechanical wave packet evolution methods

J. Andrew McCammon, Thanh N. Truong, Bogdan Lesyng, 1992 .

Fast QM/MM method and its application to molecular systems

M. Elstner, P. Bała, T. Frauenheim, 2004 .

Extended Hellmann–Feynman forces, canonical representations, and exponential propagators in the mixed quantum-classical molecular dynamics

P. Grochowski, B. Lesyng, 2003 .

Extended Hellmann-Feynman theorem for non-stationary states and its application in quantum-classical molecular dynamics simulations

James Andrew McCammon, Bogdan Lesyng, Piotr Bała, 1994 .

Theoretical investigations on the conformation of 1,5,N(4),N(4)-tetramethylcytosine.

W. Saenger, B. Lesyng, 1978, Biochimica et biophysica acta.

Prediction of secondary ionization of the phosphate group in phosphotyrosine peptides.

J. Antosiewicz, B. Lesyng, T. Grycuk, 2003, Biophysical journal.

Poisson-Boltzmann model studies of molecular electrostatic properties of the cAMP-dependent protein kinase

J. Briggs, J. Antosiewicz, J. Mccammon, 1999, European Biophysics Journal.

SCC DFT-TB energy calculations of the phosphoryl transfer reaction in the PKA active site

F. Rakowski, P. Grochowski, B. Lesyng, 2003 .

Toward the identification of molecular cogs

Bogdan Lesyng, Maciej Dziubiński, B. Lesyng, 2016, J. Comput. Chem..

EUROGRID--European computational grid testbed

Dietmar W. Erwin, Bogdan Lesyng, Piotr Bala, 2003, J. Parallel Distributed Comput..

Structure‐based sequence alignment for the β‐trefoil subdomain of the clostridial neurotoxin family provides residue level information about the putative ganglioside binding site

Č. Venclovas, K. Fidelis, K. Ginalski, 2000, FEBS letters.

Cinnamic Acid Derivatives as Inhibitors of Oncogenic Protein Kinases--Structure, Mechanisms and Biomedical Effects.

B. Lesyng, M. Mielecki, 2016, Current medicinal chemistry.

Adding numbers with DNA

Piotr Wasiewicz, Jan J. Mulawka, Witold R. Rudnicki, 2000, Smc 2000 conference proceedings. 2000 ieee international conference on systems, man and cybernetics. 'cybernetics evolving to systems, humans, organizations, and their complex interactions' (cat. no.0.

Energy of planar autoassociation of xanthine and spatial structure of poly(riboxanthylic acid)

A. Pohorille, M. Geller, B. Lesyng, 1980 .

Barrier to rotation and conformation of the -NR2 group in cytosine and its derivatives. Part II. Experimental and theoretical dipole moments of methylated cytosines.

M. Geller, B. Lesyng, K Bolewska, 1975, Biochimica et biophysica acta.

Generalized Born model: Analysis, refinement, and applications to proteins

Bogdan Lesyng, B. Lesyng, Michał Wojciechowski, 2004 .

Class IV Charge Model for the Self-Consistent Charge Density-Functional Tight-Binding Method

Donald G. Truhlar, Christopher J. Cramer, Jaroslaw Kalinowski, 2004 .

Theoretical investigations on circular and chain-like hydrogen bonded structures found in two crystal forms of α-cyclodextrin hexahydrate: Models for hydration and water clusters

W. Saenger, B. Lesyng, 1981 .

Hydrogen bonding patterns and dynamics in the hydration of biological macromolecules

C. Betzel, B. Hingerty, W. Saenger, 1985, Journal of Biosciences.

SELECTED MICROSCOPIC AND MEZOSCOPIC MODELLING TOOLS AND MODELS - AN OVERVIEW

J. Trylska, B. Lesyng, Magdalena Gruziel, 2007 .

Conformational Correlations in DNA. Molecular Dynamics Studies

B. Lesyng, W. Rudnicki, 1997 .

SP 04 Understanding the dynamics of " Pseudokinase " mutations

Christopher, Gianluigi, Lalima, 2018 .

Hydration free energy of a Model Lennard-Jones solute particle: microscopic Monte Carlo simulation studies, and interpretation based on mesoscopic models.

B. Lesyng, W. Rudnicki, Magdalena Gruziel, 2008, The Journal of chemical physics.

Car-Parrinello molecular dynamics study of the intramolecular vibrational mode-sensitive double proton-transfer mechanisms in porphycene.

B. Lesyng, J. Waluk, Łukasz Walewski, 2010, Journal of Physical Chemistry A.

Steered Classical and Quantum Path-Integral Molecular Dynamics Simulations of Strongly Coupled Protons Motions in Porphycene

P. Bała, B. Lesyng, Łukasz Walewski, 2007 .

A novel formulation of an approximate valence bond model (AVB2) and its application to the tautomeric forms of porphyrin and porphycene

P. Grochowski, B. Lesyng, M. Hallay-Suszek, 2019, Journal of Molecular Modeling.

Thermal fluctuations and infrared spectra of the formamide-formamidine complex.

B. Lesyng, J. Sadlej, Artur Smaga, 2012, The journal of physical chemistry. A.

Quantum Mechanical Simulation Methods for Studying Biological System

P. Bała, P. Grochowski, B. Lesyng, 1995 .

Structural basis of oncogenic activation caused by point mutations in the kinase domain of the MET proto‐oncogene: Modeling studies

L. Schmidt, B. Zbar, K. Ginalski, 2001, Proteins.

Binding of SPXK- and APXK-peptide motifs to AT-rich DNA. Experimental and theoretical studies.

A. Jerzmanowski, A. Lipkowski, B. Lesyng, 1998, Acta biochimica Polonica.

Molecular and Electrostatic Properties of the N-methylated Nucleic Acid Bases by Density Functional Theory

Jerzy Leszczynski, Bogdan Lesyng, Paweł Grochowski, 1996 .

Novel small molecular inhibitors disrupt the JAK/STAT3 and FAK signaling pathways and exhibit a potent antitumor activity in glioma cells

B. Kamińska, A. Ellert-Miklaszewska, J. Mieczkowski, 2012, Cancer biology & therapy.

A Mezoscopic Model of Nucleic Acids. Part 1. Lagrangian and Quaternion Molecular Dynamics

B. Lesyng, W. Rudnicki, W R Rudnicki, 2000, Journal of biomolecular structure & dynamics.

Lagrangian molecular dynamics using selected conformational degrees of freedom, with application to the pseudorotation dynamics of furanose rings

S. Harvey, B. Lesyng, W. Rudnicki, 1994, Biopolymers.

A QM-MD simulation approach to the analysis of FRET processes in (bio)molecular systems. A case study: complexes of E. coli purine nucleoside phosphorylase and its mutants with formycin A

B. Lesyng, B. Kierdaszuk, M. Kalinowski, 2015, Journal of Molecular Modeling.

Cooperative effects in extended hydrogen bonded systems involving OH groups. Ab initio studies of the cyclic S4 water tetramer

W. Saenger, B. Lesyng, J. Koehler, 1987 .

Molecular modeling methods. Basic techniques and challenging problems.

B. Lesyng, J. McCammon, 1993, Pharmacology & therapeutics.

Contributory presentations/posters

Diederichs, Bosco K. Ho, Hironori K. Nakamura, 1999, Journal of Biosciences.

SCC-DFTB Energy Barriers for Single and Double Proton Transfer Processes in the Model Molecular Systems Malonaldehyde and Porphycene

Jeremy C. Smith, S. Fischer, P. Bała, 2006 .