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List of works by Andrzej Koliński

2-Ethyl and 2-ethylidene analogues of 1alpha,25-dihydroxy-19-norvitamin D(3): synthesis, conformational analysis, biological activities, and docking to the modeled rVDR ligand binding domain

scientific article

A method for predicting protein structure from sequence.

scientific article

A minimal physically realistic protein-like lattice model: designing an energy landscape that ensures all-or-none folding to a unique native state

scientific article

A minimal proteinlike lattice model: an alpha-helix motif

scientific article published in June 2005

A new approach to prediction of short-range conformational propensities in proteins.

scientific article

A protocol for CABS-dock protein-peptide docking driven by side-chain contact information.

scientific article published on 18 August 2017

A simple lattice model that exhibits a protein-like cooperative all-or-none folding transition

scientific article published on 01 July 2003

A structure-based model fails to probe the mechanical unfolding pathways of the titin I27 domain ⬇️

scientific article published on August 14, 2013

AAindex: amino acid index database, progress report 2008

scientific article published on 12 November 2007

Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genome

scientific article

Assembly of protein structure from sparse experimental data: An efficient Monte Carlo model ⬇️

scientific article published on September 1, 1998

Backbone building from quadrilaterals: a fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates

scientific article

BioShell Threader: protein homology detection based on sequence profiles and secondary structure profiles

scientific article

BioShell--a package of tools for structural biology computations.

scientific article

BioShell-Threading: versatile Monte Carlo package for protein 3D threading.

scientific article

CABS-dock standalone: a toolbox for flexible protein-peptide docking

scientific article published on 01 October 2019

CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site

scientific article published on 5 May 2015

CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures.

scientific article published in July 2018

CABS-flex predictions of protein flexibility compared with NMR ensembles. ⬇️

scientific article published on 15 April 2014

CABS-flex standalone: a simulation environment for fast modeling of protein flexibility.

scientific article published in February 2019

CABS-flex: server for fast simulation of protein structure fluctuations ⬇️

scientific article published on May 8, 2013

CABS-fold: Server for the de novo and consensus-based prediction of protein structure

scientific article

CABS‐NMR—De novo tool for rapid global fold determination from chemical shifts, residual dipolar couplings and sparse methyl‐methyl noes ⬇️

scientific article published on August 30, 2010

Characterization of protein-folding pathways by reduced-space modeling

scientific article

ClusCo: clustering and comparison of protein models ⬇️

scientific article published on February 22, 2013

Coarse-Grained Modeling of Peptide Docking Associated with Large Conformation Transitions of the Binding Protein: Troponin I Fragment-Troponin C System.

scientific article

Coarse-Grained Modeling of Protein Dynamics

scientific article published in 2014

Coarse-Grained Modeling of the Interplay between Secondary Structure Propensities and Protein Fold Assembly

scientific article published on 27 February 2018

Coarse-Grained Protein Models and Their Applications

scientific article

Coarse-Grained Protein Models in Structure Prediction

scientific article published in 2014

Coarse-Grained Simulations of Membrane Insertion and Folding of Small Helical Proteins Using the CABS Model

scientific article published on 24 October 2016

Coarse-grained Monte Carlo simulations of mucus: structure, dynamics, and thermodynamics

scientific article published on December 2010

Coarse-grained modeling of mucus barrier properties

scientific article

Combined multiple sequence reduced protein model approach to predict the tertiary structure of small proteins ⬇️

scientific article published on January 1, 1998

Comparative modeling without implicit sequence alignments

scientific article published on 27 July 2007

Computational reconstruction of atomistic protein structures from coarse-grained models

scientific article published on 26 December 2019

Computer simulations of de novo designed helical proteins

scientific article

Computer simulations of protein folding with a small number of distance restraints

scientific article published in January 2002

Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field

scientific article published on 18 December 2012

Contact prediction in protein modeling: scoring, folding and refinement of coarse-grained models

scientific article

DNA vaccine expressing the mimotope of GD2 ganglioside induces protective GD2 cross-reactive antibody responses

scientific article

De novo simulations of the folding thermodynamics of the GCN4 leucine zipper.

scientific article

Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct?

scientific article published on March 1997

Distance matrix-based approach to protein structure prediction

scientific article

Dynamic Monte Carlo simulations of globular protein folding/unfolding pathways. I. Six-member, Greek key beta-barrel proteins

scientific article

Dynamic Monte Carlo study of the folding of a six-stranded Greek key globular protein

scientific article

Dynamics and thermodynamics of beta-hairpin assembly: insights from various simulation techniques

scientific article

Elastic network normal modes provide a basis for protein structure refinement

scientific article

Ensemble-based evaluation for protein structure models

scientific article

Erratum to: One-Dimensional Structural Properties of Proteins in the Coarse-Grained CABS Model

scientific article published in January 2017

Explicit-Solvent All-Atom Molecular Dynamics of Peptide Aggregation

scientific article published on 29 November 2018

Exploring protein energy landscapes with hierarchical clustering.

scientific article

Fast and accurate methods for predicting short-range constraints in protein models

scientific article published on 15 April 2008

Fast learning optimized prediction methodology (FLOPRED) for protein secondary structure prediction

scientific article published on 08 May 2012

Flexible docking of peptides to proteins using CABS-dock

scientific article published on 11 November 2019

Fold assembly of small proteins using Monte Carlo simulations driven by restraints derived from multiple sequence alignments ⬇️

scientific article published on March 27, 1998

Folding pathway of the b1 domain of protein G explored by multiscale modeling

scientific article

From Coarse-Grained to Atomic-Level Characterization of Protein Dynamics: Transition State for the Folding of B Domain of Protein A ⬇️

scientific article published on April 19, 2012

HCPM--program for hierarchical clustering of protein models

scientific article published on 19 April 2005

Hierarchical modeling of protein interactions.

scientific article published on 13 February 2007

High coordination lattice models of protein structure, dynamics and thermodynamics

scientific article published on January 1, 1997

Highly Flexible Protein-Peptide Docking Using CABS-Dock.

scientific article published in January 2017

How noise in force fields can affect the structural refinement of protein models?

scientific article

Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization step.

scientific article

Ideal amino acid exchange forms for approximating substitution matrices

scientific article published in November 2007

Improved method for prediction of protein backbone U-turn positions and major secondary structural elements between U-turns ⬇️

scientific article published on December 1, 1997

Improving thermal stability of thermophilic L-threonine aldolase from Thermotoga maritima.

scientific article published on 19 February 2015

Inferring ideal amino acid interaction forms from statistical protein contact potentials

scientific article published on April 2005

Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational study

scientific article published on 01 June 2018

Lattice Polymers and Protein Models

scientific article published on 13 September 2010

Mechanism of Folding and Binding of an Intrinsically Disordered Protein As Revealed by ab Initio Simulations.

scientific article

Method for low resolution prediction of small protein tertiary structure ⬇️

scientific article published on January 1, 1997

Modeling EphB4-EphrinB2 protein-protein interaction using flexible docking of a short linear motif

scientific article published on 18 August 2017

Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields ⬇️

scientific article published on 31 January 2019

Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields

scientific article published on 17 December 2018

Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models ⬇️

scientific article published on 06 November 2018

Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-grained Simulations and Elastic Network Models

scientific article published on 15 October 2018

Modeling of loops in proteins: a multi-method approach

scientific article

Modeling of protein-peptide interactions using the CABS-dock web server for binding site search and flexible docking.

scientific article published on 9 July 2015

Monte Carlo simulations of the folding of beta-barrel globular proteins ⬇️

scientific article published on July 1, 1988

Monte Carlo simulations on an equilibrium globular protein folding model

scientific article

Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models

scientific article published on 19 April 2011

Nativelike topology assembly of small proteins using predicted restraints in Monte Carlo folding simulations

scientific article published on February 1998

Note: A simple picture of subdiffusive polymer motion from stochastic simulations

scientific article published on 01 February 2011

Numerical study of the entropy loss of dimerization and the folding thermodynamics of the GCN4 leucine zipper

scientific article

Oligomerization of FVFLM peptides and their ability to inhibit beta amyloid peptides aggregation: consideration as a possible model.

scientific article published on 12 January 2017

One-Dimensional Structural Properties of Proteins in the Coarse-Grained CABS Model

scientific article

Optimization of profile-to-profile alignment parameters for one-dimensional threading

scientific article published on 25 June 2012

Predicting Real-Valued Protein Residue Fluctuation Using FlexPred

scientific article

Predicting the complex structure and functional motions of the outer membrane transporter and signal transducer FecA.

scientific article published on 4 January 2008

Prediction of protein secondary structure by neural networks: encoding short and long range patterns of amino acid packing

scientific article published on January 1, 1992

Prediction of quaternary structure of coiled coils. Application to mutants of the GCN4 leucine zipper

scientific article published on 01 August 1995

Prediction of the quaternary structure of coiled coils: GCN4 leucine zipper and its mutants ⬇️

scientific article published on January 1, 1996

Preformed template fluctuations promote fibril formation: insights from lattice and all-atom models

scientific article

Protein Dynamics Simulations Using Coarse-Grained Models

scientific article published on 29 November 2018

Protein Structure Prediction Using Coarse-Grained Models

scientific article published on 29 November 2018

Protein fragment reconstruction using various modeling techniques

scientific article published on November 2003

Protein modeling and structure prediction with a reduced representation.

scientific article published in January 2004

Protein secondary structure prediction using a small training set (compact model) combined with a Complex-valued neural network approach

scientific article

Protein structure prediction by tempering spatial constraints.

scientific article

Protein structure prediction: combining de novo modeling with sparse experimental data.

scientific article

Protein-peptide docking using CABS-dock and contact information

scientific article published on 01 November 2019

Protein-peptide docking: opportunities and challenges

scientific article published on 4 May 2018

Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction.

scientific article published on December 2016

Protein-protein docking with large-scale backbone flexibility using coarse-grained Monte-Carlo simulations

scientific article published on 23 February 2021

Protocols for All-Atom Reconstruction and High-Resolution Refinement of Protein-Peptide Complex Structures

scientific article published on 01 January 2020

Protocols for Fast Simulations of Protein Structure Flexibility Using CABS-Flex and SURPASS

scientific article published on 01 January 2020

Protocols for efficient simulations of long-time protein dynamics using coarse-grained CABS model

scientific article published in January 2014

Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes

scientific article published on 10 August 2018

SURPASS Low-Resolution Coarse-Grained Protein Modeling

scientific article

Simulation of chaperonin effect on protein folding: a shift from nucleation-condensation to framework mechanism

scientific article

Simulations of the folding pathway of triose phosphate isomerase-type alpha/beta barrel proteins

scientific article

Steps towards flexible docking: modeling of three-dimensional structures of the nuclear receptors bound with peptide ligands mimicking co-activators' sequences

scientific article published on 22 January 2007

Structural features that predict real-value fluctuations of globular proteins

scientific article

Switch from thermal to force-driven pathways of protein refolding.

scientific article published on April 2017

T-Pile--a package for thermodynamic calculations for biomolecules

scientific article published on 17 May 2007

TOUCHSTONE II: a new approach to ab initio protein structure prediction

scientific article

TOUCHSTONE: a unified approach to protein structure prediction.

scientific article

TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints.

scientific article

TOUCHSTONEX: protein structure prediction with sparse NMR data.

scientific article

Tertiary structure prediction of the KIX domain of CBP using Monte Carlo simulations driven by restraints derived from multiple sequence alignments ⬇️

scientific article published on February 15, 1998

The GOR Method of Protein Secondary Structure Prediction and Its Application as a Protein Aggregation Prediction Tool.

scientific article published in January 2017

The protein folding problem: a biophysical enigma.

scientific article

Theoretical model of prion propagation: a misfolded protein induces misfolding

scientific article

Theoretical study of molecular mechanism of binding TRAP220 coactivator to Retinoid X Receptor alpha, activated by 9-cis retinoic acid

scientific article published on 14 April 2010

Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors.

scientific article

Three-dimensional modeling of the I-TevI homing endonuclease catalytic domain, a GIY–YIG superfamily member, using NMR restraints and Monte Carlo dynamics ⬇️

scientific article published on October 1, 2001

Topology fingerprint approach to the inverse protein folding problem

scientific article

Toward more efficient simulations of slow processes in large biomolecular systems: Comment on "Ligand diffusion in proteins via enhanced sampling in molecular dynamics" by Jakub Rydzewski and Wieslaw Nowak

scientific article published in August 2017

Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field.

scientific article

Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily

scientific article

Uncharacterized DUF1574 leptospira proteins are SGNH hydrolases

scientific article

Unfolding of globular proteins: monte carlo dynamics of a realistic reduced model

scientific article

Use of residual dipolar couplings as restraints in ab initio protein structure prediction.

scientific article

Utility library for structural bioinformatics

scientific article

Why do proteins divide into domains? Insights from lattice model simulations

scientific article published on 12 October 2007

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