List of works - Adam K Sieradzan

A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. I. Backbone potentials of coarse-grained polypeptide chains

scientific article published in March 2017

A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and f

scientific article published on 01 April 2019

A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields

scientific article published on 11 October 2018

A structural model of the immune checkpoint CD160-HVEM complex derived from HDX-mass spectrometry and molecular modeling

scientific article published on 11 January 2019

A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions

scientific article

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12.

scientific article

Assessment of chemical-crosslink-assisted protein structure modeling in CASP13

scientific article published on 07 October 2019

Assessment of chemical-crosslink-assisted protein structure modeling in CASP13

scientific article published on 03 January 2020

Computational Studies of the Mechanical Stability for Single-Strand Break DNA

scientific article published on 16 August 2018

Determination of effective potentials for the stretching of C(α) ⋯ C(α) virtual bonds in polypeptide chains for coarse-grained simulations of proteins from ab initio energy surfaces of N-methylacetamide and N-acetylpyrrolidine

scientific article

Disulfide-Linked Peptides for Blocking BTLA/HVEM Binding

scientific article published on 18 January 2020

Dynamics of Disulfide-Bond Disruption and Formation in the Thermal Unfolding of Ribonuclease A.

scientific article

Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment

scientific article published on 26 July 2019

Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues

scientific article

Extension of coarse-grained UNRES force field to treat carbon nanotubes.

scientific article

Extension of the UNRES Coarse-Grained Force Field to Membrane Proteins in the Lipid Bilayer

scientific article published on 10 September 2019

Fluorescent analogs of trypsin inhibitor SFTI-1 isolated from sunflower seeds--synthesis and applications.

scientific article published on January 2014

Folding and self-assembly of a small heterotetramer

scientific article published on March 2014

Folding and self-assembly of a small protein complex

scientific article published on September 2012

Formation of Secondary and Supersecondary Structure of Proteins as a Result of Coupling Between Local and Backbone-Electrostatic Interactions: A View Through Cluster-Cumulant Scope

scientific article published on 01 January 2019

Fragments of gD Protein as Inhibitors of BTLA/HVEM Complex Formation-Design, Synthesis, and Cellular Studies

scientific article published on 23 November 2020

Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13

scientific article published on 11 February 2020

Improvement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone- and side-chain-local conformational states.

scientific article

Inhibitory activity of double-sequence analogues of trypsin inhibitor SFTI-1 from sunflower seeds: an example of peptide splicing

scientific article published on 19 April 2010

Introduction of Phosphorylated Residues into the UNRES Coarse-Grained Model: Toward Modeling of Signaling Processes

scientific article published on 26 June 2019

Introduction of periodic boundary conditions into UNRES force field

scientific article published on 08 March 2015

Introduction of steered molecular dynamics into UNRES coarse-grained simulations package.

scientific article published on 11 January 2017

Lessons from application of the UNRES force field to predictions of structures of CASP10 targets

scientific article

Molecular dynamics insights into protein-glycosaminoglycan systems from microsecond-scale simulations

scientific article published on 22 January 2019

Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction

scientific article

Peierls-Nabarro barrier and protein loop propagation. ⬇️

scientific article

Performance of protein-structure predictions with the physics-based UNRES force field in CASP11.

scientific article

Physics-Based Potentials for Coarse-Grained Modeling of Protein-DNA Interactions

scientific article published on January 2015

Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the UNited RESidue (UNRES) force field for protein simulations

scientific article

Prediction of CD28-CD86 protein complex structure using different level of resolution approach

scientific article published on 16 November 2020

Prediction of DNA and RNA structure with the NARES-2P force field and conformational space annealing

scientific article published on 01 July 2018

Revised Backbone-Virtual-Bond-Angle Potentials to Treat the l- and d-Amino Acid Residues in the Coarse-Grained United Residue (UNRES) Force Field

scientific article

Role of the sulfur to α-carbon thioether bridges in thurincin H.

scientific article published on 11 September 2016

Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers

scientific article published on 24 February 2020

Shielding effect in protein folding

scientific article published in November 2017

Structural Characterization of Covalently Stabilized Human Cystatin C Oligomers

scientific article published on 15 August 2020

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

scientific article published on 3 March 2015

The molecular mechanism of structural changes in the antimicrobial peptide CM15 upon complex formation with drug molecule suramin: a computational analysis

scientific article published on 13 May 2019

Thermal unfolding of myoglobin in the Landau-Ginzburg-Wilson approach ⬇️

scientific article published on 16 December 2016

Truncation of Huia versabilis Bowman-Birk inhibitor increases its selectivity, matriptase-1 inhibitory activity and proteolytic stability

scientific article published on 10 March 2020

UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.

scientific article published in July 2018

WeFold: a coopetition for protein structure prediction

scientific article

What Makes Telomeres Unique?

scientific article published on 14 February 2017

List of works by Adam K Sieradzan

A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. I. Backbone potentials of coarse-grained polypeptide chains

A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and f

A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields

A structural model of the immune checkpoint CD160-HVEM complex derived from HDX-mass spectrometry and molecular modeling

A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12.

Assessment of chemical-crosslink-assisted protein structure modeling in CASP13

Assessment of chemical-crosslink-assisted protein structure modeling in CASP13

Computational Studies of the Mechanical Stability for Single-Strand Break DNA

Determination of effective potentials for the stretching of C(α) ⋯ C(α) virtual bonds in polypeptide chains for coarse-grained simulations of proteins from ab initio energy surfaces of N-methylacetamide and N-acetylpyrrolidine

Disulfide-Linked Peptides for Blocking BTLA/HVEM Binding

Dynamics of Disulfide-Bond Disruption and Formation in the Thermal Unfolding of Ribonuclease A.

Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment

Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues

Extension of coarse-grained UNRES force field to treat carbon nanotubes.

Extension of the UNRES Coarse-Grained Force Field to Membrane Proteins in the Lipid Bilayer

Fluorescent analogs of trypsin inhibitor SFTI-1 isolated from sunflower seeds--synthesis and applications.

Folding and self-assembly of a small heterotetramer

Folding and self-assembly of a small protein complex

Formation of Secondary and Supersecondary Structure of Proteins as a Result of Coupling Between Local and Backbone-Electrostatic Interactions: A View Through Cluster-Cumulant Scope

Fragments of gD Protein as Inhibitors of BTLA/HVEM Complex Formation-Design, Synthesis, and Cellular Studies

Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13

Improvement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone- and side-chain-local conformational states.

Inhibitory activity of double-sequence analogues of trypsin inhibitor SFTI-1 from sunflower seeds: an example of peptide splicing

Introduction of Phosphorylated Residues into the UNRES Coarse-Grained Model: Toward Modeling of Signaling Processes

Introduction of periodic boundary conditions into UNRES force field

Introduction of steered molecular dynamics into UNRES coarse-grained simulations package.

Lessons from application of the UNRES force field to predictions of structures of CASP10 targets

Molecular dynamics insights into protein-glycosaminoglycan systems from microsecond-scale simulations

Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction

Peierls-Nabarro barrier and protein loop propagation. ⬇️

Performance of protein-structure predictions with the physics-based UNRES force field in CASP11.

Physics-Based Potentials for Coarse-Grained Modeling of Protein-DNA Interactions

Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the UNited RESidue (UNRES) force field for protein simulations

Prediction of CD28-CD86 protein complex structure using different level of resolution approach

Prediction of DNA and RNA structure with the NARES-2P force field and conformational space annealing

Revised Backbone-Virtual-Bond-Angle Potentials to Treat the l- and d-Amino Acid Residues in the Coarse-Grained United Residue (UNRES) Force Field

Role of the sulfur to α-carbon thioether bridges in thurincin H.

Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers

Shielding effect in protein folding

Structural Characterization of Covalently Stabilized Human Cystatin C Oligomers

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

The molecular mechanism of structural changes in the antimicrobial peptide CM15 upon complex formation with drug molecule suramin: a computational analysis

Thermal unfolding of myoglobin in the Landau-Ginzburg-Wilson approach ⬇️

Truncation of Huia versabilis Bowman-Birk inhibitor increases its selectivity, matriptase-1 inhibitory activity and proteolytic stability

UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.

WeFold: a coopetition for protein structure prediction

What Makes Telomeres Unique?