D. Nolde

发表

Increasing normal modes analysis accuracy: The SPASIBA spectroscopic force field introduced into the CHARMM program

M. Karplus, R. Stote, G. Vergoten, 2004 .

A Solvent Model for Simulations of Peptides in Bilayers. I. Membrane-Promoting α-Helix Formation

Roman G. Efremov, Dmitry E. Nolde, Alexander S. Arseniev, 1999 .

Peptides and proteins in membranes: what can we learn via computer simulations?

D. Nolde, A. Arseniev, R. Efremov, 2004, Current medicinal chemistry.

Temperature-sensitive gating of TRPV1 channel as probed by atomistic simulations of its trans- and juxtamembrane domains

D. Nolde, R. Efremov, P. Volynsky, 2016, Scientific Reports.

Peptides in membranes: assessment of environmental effects via simulations using an implicit solvation model

G. Vergoten, D. Nolde, A. Arseniev, 1999 .

Three-dimensional structure of ectatomin from Ectatomma tuberculatum ant venom

E. Grishin, D. Nolde, A. Arseniev, 1995, Journal of biomolecular NMR.

Toxic principle of selva ant venom is a pore‐forming protein transformer

S. V. Sukhanov, E. Grishin, D. Nolde, 1994, FEBS letters.

Membrane-mediated interaction of non-conventional snake three-finger toxins with nicotinic acetylcholine receptors

D. Nolde, M. Kirpichnikov, E. Lyukmanova, 2022, Communications Biology.

Structure-based rational design of an enhanced fluorogen-activating protein for fluorogens based on GFP chromophore

M. V. Goncharuk, D. Nolde, M. Baranov, 2022, Communications Biology.

Interaction of cardiotoxins with membranes: a molecular modeling study.

Roman G Efremov, D. Nolde, A. Arseniev, 2002, Biophysical journal.

Molecular modelling of the nucleotide-binding domain of Wilson's disease protein: location of the ATP-binding site, domain dynamics and potential effects of the major disease mutations.

D. Nolde, A. Arseniev, Yurij A. Kosinsky, 2004, The Biochemical journal.

Processing of heteronuclear NMR relaxation data with the new software DASHA

D. Nolde, V. Orekhov, A. Arseniev, 1995 .

Role of lipid charge in organization of water/lipid bilayer interface: insights via computer simulations.

D. Nolde, A. Arseniev, R. Efremov, 2005, The journal of physical chemistry. B.

Method To Assess Packing Quality of Transmembrane α-Helices in Proteins, 1. Parametrization Using Structural Data

Roman G. Efremov, Anton O. Chugunov, Valery N. Novoseletsky, 2007, J. Chem. Inf. Model..

Method To Assess Packing Quality of Transmembrane α-Helices in Proteins, 2. Validation by "Correct vs Misleading" Test

Roman G. Efremov, Anton O. Chugunov, Valery N. Novoseletsky, 2007, J. Chem. Inf. Model..

Modeling of Peptides in Implicit Membrane-Mimetic Media

D. Nolde, A. Arseniev, R. Efremov, 2000 .

A Solvent Model for Simulations of Peptides in Bilayers. II. Membrane-Spanning α-Helices

Roman G. Efremov, Dmitry E. Nolde, Alexander S. Arseniev, 1999 .

Three‐dimensional structure of binase in solution

D. Nolde, A. Arseniev, M. Reibarkh, 1998, FEBS letters.

PLATINUM: a web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes

Roman G. Efremov, Anton O. Chugunov, Dmitry E. Nolde, 2009, Bioinform..

PREDDIMER: a web server for prediction of transmembrane helical dimers

Roman G. Efremov, Anton O. Chugunov, Dmitry E. Nolde, 2014, Bioinform..

Specific refolding pathway of viscumin A chain in membrane-like medium reveals a possible mechanism of toxin entry into cell

D. Nolde, A. Tonevitsky, R. Efremov, 2019, Scientific Reports.

Lipid-II forms potential “landing terrain” for lantibiotics in simulated bacterial membrane

D. Nolde, R. Efremov, A. Polyansky, 2013, Scientific Reports.

Specificity of helix packing in transmembrane dimer of the cell death factor BNIP3: A molecular modeling study

Yana A. Vereshaga, D. Nolde, A. Arseniev, 2007, Proteins.

Three-dimensional structure of proteolytic fragment 163-231 of bacterioopsin determined from nuclear magnetic resonance data in solution.

D. Nolde, A. Arseniev, A. Lomize, 1992, European journal of biochemistry.

Three-dimensional structure of toxin OSK1 from Orthochirus scrobiculosus scorpion venom.

E. Grishin, D. Nolde, A. Arseniev, 1997, Biochemistry.

Fusion Peptide Interaction with Lipid Bilayer: Modeling with Monte Carlo Simulation and Continuum Electrostatics Calculation

D. Nolde, A. Arseniev, Yurij A. Kosinsky, 2000 .

Factors important for fusogenic activity of peptides: molecular modeling study of analogs of fusion peptide of influenza virus hemagglutinin

D. Nolde, A. Arseniev, R. Efremov, 1999, FEBS letters.

Implicit two-phase solvation model as a tool to assess conformation and energetics of proteins in membrane-mimetic media

G. Vergoten, D. Nolde, A. Arseniev, 2001 .

Environmental and dynamic effects explain how nisin captures membrane-bound lipid II

D. Nolde, R. Efremov, A. Chugunov, 2020, Scientific Reports.

Atomic solvation parameters for proteins in a membrane environment. Application to transmembrane alpha-helices.

G. Vergoten, D. Nolde, A. Arseniev, 1997, Journal of biomolecular structure & dynamics.

Dynamic clustering of lipids in hydrated two-component membranes: results of computer modeling and putative biological impact

D. Nolde, R. Efremov, N. Krylov, 2013, Journal of biomolecular structure & dynamics.

A solvent model for simulations of peptides in bilayers. II. Membrane-spanning alpha-helices.

G. Vergoten, D. Nolde, A. Arseniev, 1999, Biophysical journal.

The Membrane-proximal Fusion Domain of HIV-1 GP41 Reveals Sequence-specific and Fine-tuning Mechanism of Membrane Binding

G. Vergoten, D. Nolde, A. Arseniev, 2007, Journal of biomolecular structure & dynamics.