On the need to introduce environmental characteristics in ab initio protein structure prediction using a coarse-grained UNRES force field

Model of Environmental Membrane Field for Transmembrane Proteins

(2021) Irena Roterman et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Investigation of Phosphorylation-Induced Folding of an Intrinsically Disordered Protein by Coarse-Grained Molecular Dynamics

(2021) Adam K. Sieradzan et al.   Journal of Chemical Theory and Computation

The Functional Significance of Hydrophobic Residue Distribution in Bacterial Beta-Barrel Transmembrane Proteins

(2021) Irena Roterman et al.   Membranes

On the Dependence of Prion and Amyloid Structure on the Folding Environment

(2021) Irena Roterman et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

In Silico Modeling of the Influence of Environment on Amyloid Folding Using FOD-M Model

(2021) Irena Roterman et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

(2020) Agnieszka S. Karczyńska et al.   Journal of Chemical Information and Modeling

Alternative Structures of α-Synuclein

(2020) Dawid Dułak et al.   MOLECULES

Alternative Hydrophobic Core in Proteins—The Effect of Specific Synergy

(2020) Piotr Fabian et al.   Symmetry-Basel

Structure of the Hydrophobic Core Determines the 3D Protein Structure—Verification by Single Mutation Proteins

(2020) Mateusz Banach et al.   Biomolecules

The Structure of Amyloid Versus the Structure of Globular Proteins

(2020) Piotr Fabian et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

ProteinUnet —An efficient alternative to SPIDER3‐single for sequence‐based prediction of protein secondary structures

(2020) Krzysztof Kotowski et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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 force-field calibration and validation

(2019) Adam Liwo et al.   JOURNAL OF CHEMICAL PHYSICS

Structural analysis of the Aβ(11–42) amyloid fibril based on hydrophobicity distribution

(2019) Irena Roterman et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Critical assessment of methods of protein structure prediction (CASP)—Round XIII

(2019) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Shielding effect in protein folding

(2018) Adam K. Sieradzan et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Filamentous Aggregates of Tau Proteins Fulfil Standard Amyloid Criteria Provided by the Fuzzy Oil Drop (FOD) Model

(2018) Dawid Dułak et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The aqueous environment as an active participant in the protein folding process

(2018) Małgorzata Gadzała et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

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

(2017) Adam K. Sieradzan et al.   JOURNAL OF CHEMICAL PHYSICS

Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged–Hydrophobic/Polar and Polar–Hydrophobic/Polar Side Chains

(2017) Mariusz Makowski et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Multiscale modeling of a rectifying bipolar nanopore: explicit-water versus implicit-water simulations

(2017) Zoltán Ható et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Application of Divergence Entropy to Characterize the Structure of the Hydrophobic Core in DNA Interacting Proteins

(2015) Barbara Kalinowska et al.   Entropy

Physics-Based Potentials for the Coupling between Backbone- and Side-Chain-Local Conformational States in the United Residue (UNRES) Force Field for Protein Simulations

(2015) Adam K. Sieradzan et al.   Journal of Chemical Theory and Computation

Modeling Protein–Micelle Systems in Implicit Water

(2015) Rodney E. Versace et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Shaking Alone Induces De Novo Conversion of Recombinant Prion Proteins to β-Sheet Rich Oligomers and Fibrils

(2014) Carol L. Ladner-Keay et al.   PLoS One

WeFold: A coopetition for protein structure prediction

(2014) George A. Khoury et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Determination of Effective Potentials for the Stretching of Cα···Cα Virtual Bonds in Polypeptide Chains for Coarse-Grained Simulations of Proteins from ab Initio Energy Surfaces of N-Methylacetamide and N-Acetylpyrrolidine

(2012) Adam K. Sieradzan et al.   Journal of Chemical Theory and Computation

Structure and properties of the metastable bacteriocin Lcn972 from Lactococcus lactis

(2012) David L. Turner et al.   JOURNAL OF MOLECULAR STRUCTURE

Two-intermediate model to characterize the structure of fast-folding proteins

(2011) I. Roterman et al.   JOURNAL OF THEORETICAL BIOLOGY

Coarse-grained force field: general folding theory

(2011) Adam Liwo et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Fast procedure for reconstruction of full-atom protein models from reduced representations

(2008) Piotr Rotkiewicz et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Principal Component Analysis for Protein Folding Dynamics

(2008) Gia G. Maisuradze et al.   JOURNAL OF MOLECULAR BIOLOGY

NMR structures of two designed proteins with high sequence identity but different fold and function

(2008) Y. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA