List of works - Andrzej Kloczkowski

A Consensus Data Mining secondary structure prediction by combining GOR V and Fragment Database Mining

scientific article

A DNA-Centric Look at Protein-DNA Complexes

article

A Hybrid Levenberg-Marquardt Algorithm on a Recursive Neural Network for Scoring Protein Models

scientific article published on 01 January 2021

A global machine learning based scoring function for protein structure prediction.

scientific article

A novel orientation technique for semi-rigid polymers. 2. Mechanical properties of cellulose acetate and hydroxypropylcellulose films

A topological order parameter for describing folding free energy landscapes of proteins

scientific article published on 01 November 2018

Accurate Prediction of One-Dimensional Protein Structure Features Using SPINE-X.

scientific article

Accurate single-sequence prediction of solvent accessible surface area using local and global features

scientific article

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

scientific article

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

scientific article

Chain dimensions and fluctuations in elastomeric networks in which the junctions alternate regularly in their functionality

scientific article published on February 2009

Combining statistical potentials with dynamics-based entropies improves selection from protein decoys and docking poses

scientific article

Comparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder

scientific article published on 17 July 2017

Conditional entropy in variation-adjusted windows detects selection signatures associated with expression quantitative trait loci (eQTLs).

scientific article published on 18 June 2015

Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: combining GOR V and Fragment Database Mining (FDM)

scientific article

Data Mining for Protein Secondary Structure Prediction

DescribePROT: database of amino acid-level protein structure and function predictions

scientific article published on 29 October 2020

Distance matrix-based approach to protein structure prediction

scientific article

Effects of protein subunits removal on the computed motions of partial 30S structures of the ribosome

scientific article published in September 2008

Elastic network normal modes provide a basis for protein structure refinement

scientific article

Entropy, Fluctuations, and Disordered Proteins

scientific article published on 06 August 2019

Explicit-Solvent All-Atom Molecular Dynamics of Peptide Aggregation

scientific article published on 29 November 2018

Exploration of the relationship between topology and designability of conformations

scientific article published on June 2011

Fast and Accurate Accessible Surface Area Prediction Without a Sequence Profile

scientific article

Filler-induced deformations of amorphous polyethylene chains. The effects of the deformations on elastomeric properties, and some comparisons with experiments

Fold-specific sequence scoring improves protein sequence matching

scientific article

Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys.

scientific article published in July 2007

Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models.

scientific article

Functional clustering of yeast proteins from the protein-protein interaction network

scientific article

GENN: a GEneral Neural Network for learning tabulated data with examples from protein structure prediction.

scientific article

GOR V server for protein secondary structure prediction

scientific article

Generation and enumeration of compact conformations on the two-dimensional triangular and three-dimensional fcc lattices

article

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

Immunoglobulin Structure Exhibits Control over CDR Motion

scientific article

In silico modeling of human α2C-adrenoreceptor interaction with filamin-2

scientific article

Inferring ideal amino acid interaction forms from statistical protein contact potentials

scientific article published on April 2005

Innovations in Genomics and Big Data Analytics for Personalized Medicine and Health Care: A Review

publication published on 22 April 2022

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

Loop folds in proteins and evolutionary conservation of folding nuclei

scientific article published on 01 December 2002

MAVENs: motion analysis and visualization of elastic networks and structural ensembles

scientific article

MQAPsingle: A quasi single-model approach for estimation of the quality of individual protein structure models.

scientific article

Many-to-one binding by intrinsically disordered protein regions

scientific article published on 01 January 2020

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 the elastomeric properties of stereoregular polypropylenes in nanocomposites with spherical fillers

Models to Approximate the Motions of Protein Loops

scientific article

Molecular modeling of matrix chain deformation in nanofiber filled composites

Molecular modeling of phosphorylation sites in proteins using a database of local structure segments

scientific article

Monte Carlo Simulations on Nanoparticles in Elastomers. Effects of the Particles on the Dimensions of the Polymer Chains and the Mechanical Properties of the Networks

Multi-class BCGA-ELM based classifier that identifies biomarkers associated with hallmarks of cancer

scientific article published on 20 May 2015

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

scientific article published on 19 April 2011

Orientational distributions of contact clusters in proteins closely resemble those of an icosahedron

scientific article published on November 2008

P.R.E.S.S.--an R-package for exploring residual-level protein structural statistics

scientific article published on June 2012

Packing regularities in biological structures relate to their dynamics

scientific article

Potentials 'R' Us web-server for protein energy estimations with coarse-grained knowledge-based potentials ⬇️

scientific article

Predicting Designability of Small Proteins from Graph Features of Contact Maps

scientific article

Predicting binding sites of hydrolase-inhibitor complexes by combining several methods

scientific article

Predicting protein tertiary structure and its uncertainty analysis via particle swarm sampling

scientific article published on 27 February 2019

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

scientific article published on 4 January 2008

Predicting the order in which contacts are broken during single molecule protein stretching experiments

scientific article

Prediction of Protein Tertiary Structure via Regularized Template Classification Techniques

scientific article published on 26 May 2020

Prediction of Site Directed miRNAs as Key Players of Transcriptional Regulators Against Influenza C Virus Infection Through Computational Approaches

scientific article published on 08 April 2022

Prediction of protein secondary structure by mining structural fragment database

scientific article published on May 2005

Prediction of side chain orientations in proteins by statistical machine learning methods.

scientific article

Principal component analysis in protein tertiary structure prediction.

scientific article published on 22 February 2018

Protein promiscuity: drug resistance and native functions--HIV-1 case

scientific article published in June 2005

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

scientific article

Reoptimized UNRES Potential for Protein Model Quality Assessment

article

Robust Prediction of Single and Multiple Point Protein Mutations Stability Changes

scientific article published on 31 December 2019

Robust Sampling of Defective Pathways in Alzheimer’s Disease. Implications in Drug Repositioning ⬇️

journal article from 'International Journal of Molecular Sciences' published in 2020

Robust Sampling of Defective Pathways in Multiple Myeloma

scientific article published on 21 September 2019

Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes

scientific article published on 10 August 2018

Shape-dependent designability studies of lattice proteins

scientific article published on July 2007

Short paths in protein structure space originate in graph structure

scientific article published on 14 December 2009

Some simulations on filler reinforcement in elastomers

Statistical measures on residue-level protein structural properties

scientific article published on 31 March 2011

Structural interpretation of protein-protein interaction network

scientific article

Support-vector-machine classification of linear functional motifs in proteins.

scientific article

The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models

scientific article published on January 2006

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

scientific article published in January 2017

The energy profiles of atomic conformational transition intermediates of adenylate kinase

scientific article

The importance of slow motions for protein functional loops

scientific article published on 07 February 2012

The largest eigenvalue method for stereo-regular vinyl chains

The origin and extent of coarse-grained regularities in protein internal packing

scientific article

The ribosome structure controls and directs mRNA entry, translocation and exit dynamics

scientific article published on 24 November 2008

The transfer matrix method for lattice proteins—an application with cooperative interactions

Use of machine learning algorithms to classify binary protein sequences as highly-designable or poorly-designable

scientific article

Volumes and surface areas: geometries and scaling relationships between coarse- grained and atomic structures

scientific article published on January 2014

List of works by Andrzej Kloczkowski

A Consensus Data Mining secondary structure prediction by combining GOR V and Fragment Database Mining

A DNA-Centric Look at Protein-DNA Complexes

A Hybrid Levenberg-Marquardt Algorithm on a Recursive Neural Network for Scoring Protein Models

A global machine learning based scoring function for protein structure prediction.

A novel orientation technique for semi-rigid polymers. 2. Mechanical properties of cellulose acetate and hydroxypropylcellulose films

A topological order parameter for describing folding free energy landscapes of proteins

Accurate Prediction of One-Dimensional Protein Structure Features Using SPINE-X.

Accurate single-sequence prediction of solvent accessible surface area using local and global features

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

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

Chain dimensions and fluctuations in elastomeric networks in which the junctions alternate regularly in their functionality

Combining statistical potentials with dynamics-based entropies improves selection from protein decoys and docking poses

Comparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder

Conditional entropy in variation-adjusted windows detects selection signatures associated with expression quantitative trait loci (eQTLs).

Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: combining GOR V and Fragment Database Mining (FDM)

Data Mining for Protein Secondary Structure Prediction

DescribePROT: database of amino acid-level protein structure and function predictions

Distance matrix-based approach to protein structure prediction

Effects of protein subunits removal on the computed motions of partial 30S structures of the ribosome

Elastic network normal modes provide a basis for protein structure refinement

Entropy, Fluctuations, and Disordered Proteins

Explicit-Solvent All-Atom Molecular Dynamics of Peptide Aggregation

Exploration of the relationship between topology and designability of conformations

Fast and Accurate Accessible Surface Area Prediction Without a Sequence Profile

Filler-induced deformations of amorphous polyethylene chains. The effects of the deformations on elastomeric properties, and some comparisons with experiments

Fold-specific sequence scoring improves protein sequence matching

Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys.

Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models.

Functional clustering of yeast proteins from the protein-protein interaction network

GENN: a GEneral Neural Network for learning tabulated data with examples from protein structure prediction.

GOR V server for protein secondary structure prediction

Generation and enumeration of compact conformations on the two-dimensional triangular and three-dimensional fcc lattices

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

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

Ideal amino acid exchange forms for approximating substitution matrices.

Immunoglobulin Structure Exhibits Control over CDR Motion

In silico modeling of human α2C-adrenoreceptor interaction with filamin-2

Inferring ideal amino acid interaction forms from statistical protein contact potentials

Innovations in Genomics and Big Data Analytics for Personalized Medicine and Health Care: A Review

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

Loop folds in proteins and evolutionary conservation of folding nuclei

MAVENs: motion analysis and visualization of elastic networks and structural ensembles

MQAPsingle: A quasi single-model approach for estimation of the quality of individual protein structure models.

Many-to-one binding by intrinsically disordered protein regions

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

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

Modeling the elastomeric properties of stereoregular polypropylenes in nanocomposites with spherical fillers

Models to Approximate the Motions of Protein Loops

Molecular modeling of matrix chain deformation in nanofiber filled composites

Molecular modeling of phosphorylation sites in proteins using a database of local structure segments

Monte Carlo Simulations on Nanoparticles in Elastomers. Effects of the Particles on the Dimensions of the Polymer Chains and the Mechanical Properties of the Networks

Multi-class BCGA-ELM based classifier that identifies biomarkers associated with hallmarks of cancer

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

Orientational distributions of contact clusters in proteins closely resemble those of an icosahedron

P.R.E.S.S.--an R-package for exploring residual-level protein structural statistics

Packing regularities in biological structures relate to their dynamics

Potentials 'R' Us web-server for protein energy estimations with coarse-grained knowledge-based potentials ⬇️

Predicting Designability of Small Proteins from Graph Features of Contact Maps

Predicting binding sites of hydrolase-inhibitor complexes by combining several methods

Predicting protein tertiary structure and its uncertainty analysis via particle swarm sampling

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

Predicting the order in which contacts are broken during single molecule protein stretching experiments

Prediction of Protein Tertiary Structure via Regularized Template Classification Techniques

Prediction of Site Directed miRNAs as Key Players of Transcriptional Regulators Against Influenza C Virus Infection Through Computational Approaches

Prediction of protein secondary structure by mining structural fragment database

Prediction of side chain orientations in proteins by statistical machine learning methods.

Principal component analysis in protein tertiary structure prediction.

Protein promiscuity: drug resistance and native functions--HIV-1 case

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

Reoptimized UNRES Potential for Protein Model Quality Assessment

Robust Prediction of Single and Multiple Point Protein Mutations Stability Changes

Robust Sampling of Defective Pathways in Alzheimer’s Disease. Implications in Drug Repositioning ⬇️

Robust Sampling of Defective Pathways in Multiple Myeloma

Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes

Shape-dependent designability studies of lattice proteins

Short paths in protein structure space originate in graph structure

Some simulations on filler reinforcement in elastomers

Statistical measures on residue-level protein structural properties

Structural interpretation of protein-protein interaction network