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Andrzej Kolinski

Research Profile

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Physiology

Protein Folding

Chemicals & Drugs

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Genes & Molecular Sequences

Amino Acid Sequences

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Publications

TOP 3
Michal Jamroz; Andrzej Kolinski
ClusCo: clustering and comparison of protein models.
Pawel Gniewek; Andrzej Kolinski; Dominik Gront
Optimization of profile-to-profile alignment parameters for one-dimensional threading.
Dominik Gront; Maciej Blaszczyk; Piotr Wojciechowski; Andrzej Kolinski
BioShell Threader: protein homology detection based on sequence profiles and secondary structure profiles.

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All Publications

2013: Michal Jamroz; Andrzej Kolinski
ClusCo: clustering and comparison of protein models.
BMC bioinformatics 2013;14():62.
2012: Pawel Gniewek; Andrzej Kolinski; Dominik Gront
Optimization of profile-to-profile alignment parameters for one-dimensional threading.
Journal of computational biology : a journal of computational molecular cell biology 2012;19(7):879-86.
2012: Dominik Gront; Maciej Blaszczyk; Piotr Wojciechowski; Andrzej Kolinski
BioShell Threader: protein homology detection based on sequence profiles and secondary structure profiles.
Nucleic acids research 2012;40(Web Server issue):W257-62.
2012: Sebastian Kmiecik; Dominik Gront; Maksim Kouza; Andrzej Kolinski
From coarse-grained to atomic-level characterization of protein dynamics: transition state for the folding of B domain of protein A.
The journal of physical chemistry. B 2012;116(23):7026-32.
2012: Pawel Gniewek; Robert L Jernigan; Andrzej Kolinski; Andrzej Kloczkowski
Elastic network normal modes provide a basis for protein structure refinement.
The Journal of chemical physics 2012;136(19):195101.
2012: Michal Jamroz; Andrzej Kolinski; Daisuke Kihara
Structural features that predict real-value fluctuations of globular proteins.
Proteins 2012;80(5):1425-35.
2012: Pawel Gniewek; Andrzej Kolinski
Coarse-grained modeling of mucus barrier properties.
Biophysical journal 2012;102(2):195-200.
2012: Karol Kamel; Andrzej Kolinski
Assessment of the free binding energy of 1,25-dihydroxyvitamin D3 and its analogs with the human VDR receptor model.
Acta biochimica Polonica 2012;59(4):653-60.
2011: Sebastian Kmiecik; Andrzej Kolinski
Simulation of chaperonin effect on protein folding: a shift from nucleation-condensation to framework mechanism.
Journal of the American Chemical Society 2011;133(26):10283-9.
2011: Kamil Steczkiewicz; Michael T Zimmermann; Drena Dobbs; Robert L Jernigan; Andrzej Kloczkowski; Andrzej Kolinski; Mateusz Kurcinski; Benjamin A Lewis; Krzysztof Ginalski
Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization step.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(23):9443-8.
2011: Pawel Gniewek; Sumudu P Leelananda; Andrzej Kolinski; Robert L Jernigan; Andrzej Kloczkowski
Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models.
Proteins 2011;79(6):1923-9.
2011: Dorota Latek; Andrzej Kolinski
CABS-NMR--De novo tool for rapid global fold determination from chemical shifts, residual dipolar couplings and sparse methyl-methyl NOEs.
Journal of computational chemistry 2011;32(3):536-44.
2011: Karol Kamel; Andrzej Kolinski
Computational study of binding of epothilone A to β-tubulin.
Acta biochimica Polonica 2011;58(2):255-60.
2010: Pawel Gniewek; Andrzej Kolinski
Coarse-grained Monte Carlo simulations of mucus: structure, dynamics, and thermodynamics.
Biophysical journal 2010;99(11):3507-16.
2010: Mateusz Kurcinski; Andrzej Kolinski
Theoretical study of molecular mechanism of binding TRAP220 coactivator to Retinoid X Receptor alpha, activated by 9-cis retinoic acid.
The Journal of steroid biochemistry and molecular biology 2010;121(1-2):124-9.
2010: Sebastian Trojanowski; Aleksandra Rutkowska; Andrzej Kolinski
TRACER. A new approach to comparative modeling that combines threading with free-space conformational sampling.
Acta biochimica Polonica 2010;57(1):125-33.
2010: Michal Jamroz; Andrzej Kolinski
Modeling of loops in proteins: a multi-method approach.
BMC structural biology 2010;10():5.
2009: Andrzej Kloczkowski; Robert L Jernigan; Zhijun Wu; Guang Song; Lei Yang; Andrzej Kolinski; Piotr Pokarowski
Distance matrix-based approach to protein structure prediction.
Journal of structural and functional genomics 2009;10(1):67-81.
2008: Dominik Gront; Andrzej Kolinski
Fast and accurate methods for predicting short-range constraints in protein models.
Journal of computer-aided molecular design 2008;22(11):783-8.
2008: Taner Z Sen; Margaret Kloster; Robert L Jernigan; Andrzej Kolinski; Janusz Bujnicki; Andrzej Kloczkowski
Predicting the complex structure and functional motions of the outer membrane transporter and signal transducer FecA.
Biophysical journal 2008;94(7):2482-91.
2008: Lukasz Knizewski; Kamil Steczkiewicz; Krzysztof Kuchta; Lucjan Wyrwicz; Dariusz Plewczynski; Andrzej Kolinski; Leszek Rychlewski; Krzysztof Ginalski
Uncharacterized DUF1574 leptospira proteins are SGNH hydrolases.
Cell cycle (Georgetown, Tex.) 2008;7(4):542-4.
2008: Dominik Gront; Andrzej Kolinski
Utility library for structural bioinformatics.
Bioinformatics (Oxford, England) 2008;24(4):584-5.
2008: Sebastian Kmiecik; Andrzej Kolinski
Folding pathway of the b1 domain of protein G explored by multiscale modeling.
Biophysical journal 2008;94(3):726-36.
2008: Dorota Latek; Andrzej Kolinski
Contact prediction in protein modeling: scoring, folding and refinement of coarse-grained models.
BMC structural biology 2008;8():36.
2008: Shuichi Kawashima; Piotr Pokarowski; Maria Pokarowska; Andrzej Kolinski; Toshiaki Katayama; Minoru Kanehisa
AAindex: amino acid index database, progress report 2008.
Nucleic acids research 2008;36(Database issue):D202-5.
2007: Aleksandra Rutkowska; Andrzej Kolinski
Why do proteins divide into domains? Insights from lattice model simulations.
Biomacromolecules 2007;8(11):3519-24.
2007: Piotr Pokarowski; Andrzej Kloczkowski; Szymon Nowakowski; Maria Pokarowska; Robert L Jernigan; Andrzej Kolinski
Ideal amino acid exchange forms for approximating substitution matrices.
Proteins 2007;69(2):379-93.
2007: Andrzej Kolinski; Dominik Gront
Comparative modeling without implicit sequence alignments.
Bioinformatics (Oxford, England) 2007;23(19):2522-7.
2007: Dorota Latek; Dariusz Ekonomiuk; Andrzej Kolinski
Protein structure prediction: combining de novo modeling with sparse experimental data.
Journal of computational chemistry 2007;28(10):1668-76.
2007: Sebastian Kmiecik; Andrzej Kolinski
Characterization of protein-folding pathways by reduced-space modeling.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(30):12330-5.
2007: Dominik Gront; Andrzej Kolinski
T-Pile--a package for thermodynamic calculations for biomolecules.
Bioinformatics (Oxford, England) 2007;23(14):1840-2.
2007: Dominik Gront; Sebastian Kmiecik; Andrzej Kolinski
Backbone building from quadrilaterals: a fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates.
Journal of computational chemistry 2007;28(9):1593-7.
2007: Mateusz Kurcinski; Andrzej Kolinski
Hierarchical modeling of protein interactions.
Journal of molecular modeling 2007;13(6-7):691-8.
2007: Mateusz Kurcinski; Andrzej Kolinski
Steps towards flexible docking: modeling of three-dimensional structures of the nuclear receptors bound with peptide ligands mimicking co-activators' sequences.
The Journal of steroid biochemistry and molecular biology 2007;103(3-5):357-60.
2007: Elena M Ibryashkina; Marina Zakharova; Vladimir B Baskunov; Ekaterina S Bogdanova; Maxim O Nagornykh; Marat M Den'mukhamedov; Bogdan S Melnik; Andrzej Kolinski; Dominik Gront; Marcin Feder; Alexander S Solonin; Janusz Bujnicki
Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily.
BMC structural biology 2007;7():48.
2007: Sebastian Kmiecik; Dominik Gront; Andrzej Kolinski
Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field.
BMC structural biology 2007;7():43.
2006: Dominik Gront; Mateusz Kurcinski; Andrzej Kolinski
Clustering as a supporting tool for structural drug design.
Acta poloniae pharmaceutica 2006;63(5):436-8.
2006: Marcin Hoffmann; Krystian Eitner; Marcin von Grotthuss; Leszek Rychlewski; Ewa Banachowicz; Tomasz Grabarkiewicz; Tomasz Szkoda; Andrzej Kolinski
Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors.
Journal of computer-aided molecular design 2006;20(5):305-19.
2006: Dominik Gront; Andrzej Kolinski
BioShell--a package of tools for structural biology computations.
Bioinformatics (Oxford, England) 2006;22(5):621-2.
2006: Sebastian Kmiecik; Mateusz Kurcinski; Aleksandra Rutkowska; Dominik Gront; Andrzej Kolinski
Denatured proteins and early folding intermediates simulated in a reduced conformational space.
Acta biochimica Polonica 2006;53(1):131-44.
2005: Dominik Gront; Andrzej Kolinski; Ulrich H E Hansmann
Protein structure prediction by tempering spatial constraints.
Journal of computer-aided molecular design 2005;19(8):603-8.
2005: Dominik Gront; Andrzej Kolinski
HCPM--program for hierarchical clustering of protein models.
Bioinformatics (Oxford, England) 2005;21(14):3179-80.
2005: Piotr Pokarowski; Karol Droste; Andrzej Kolinski
A minimal proteinlike lattice model: an alpha-helix motif.
The Journal of chemical physics 2005;122(21):214915.
2005: Edyta Małolepsza; Michal Boniecki; Andrzej Kolinski; Lucjan Piela
Theoretical model of prion propagation: a misfolded protein induces misfolding.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(22):7835-40.
2005: Elizabeth Bolesta; Aleksandra Kowalczyk; Andrzej Wierzbicki; Piotr Rotkiewicz; Barbara Bambach; Chun-Yen Tsao; Irena Horwacik; Andrzej Kolinski; Hanna Rokita; Martin Brecher; Xinhui Wang; Soldano Ferrone; Danuta Kozbor
DNA vaccine expressing the mimotope of GD2 ganglioside induces protective GD2 cross-reactive antibody responses.
Cancer research 2005;65(8):3410-8.
2005: Piotr Pokarowski; Andrzej Kloczkowski; Robert L Jernigan; Neha S Kothari; Maria Pokarowska; Andrzej Kolinski
Inferring ideal amino acid interaction forms from statistical protein contact potentials.
Proteins 2005;59(1):49-57.
2005: Dominik Gront; Andrzej Kolinski
A new approach to prediction of short-range conformational propensities in proteins.
Bioinformatics (Oxford, England) 2005;21(7):981-7.
2005: Dariusz Ekonomiuk; Marcin Kielbasinski; Andrzej Kolinski
Protein modeling with reduced representation: statistical potentials and protein folding mechanism.
Acta biochimica Polonica 2005;52(4):741-8.
2004: Andrzej Kolinski
Protein modeling and structure prediction with a reduced representation.
Acta biochimica Polonica 2004;51(2):349-71.
2003: Turkan Haliloglu; Andrzej Kolinski; Jeffrey Skolnick
Use of residual dipolar couplings as restraints in ab initio protein structure prediction.
Biopolymers 2003;70(4):548-62.
2003: Michal Boniecki; Piotr Rotkiewicz; Jeffrey Skolnick; Andrzej Kolinski
Protein fragment reconstruction using various modeling techniques.
Journal of computer-aided molecular design 2003;17(11):725-38.
2003: Andrzej Kolinski; Piotr Klein; Piotr Romiszowski; Jeffrey Skolnick
Unfolding of globular proteins: monte carlo dynamics of a realistic reduced model.
Biophysical journal 2003;85(5):3271-8.
2003: Wei Li; Yang Zhang; Daisuke Kihara; Yuanpeng J Huang; Deyou Zheng; Gaetano T Montelione; Andrzej Kolinski; Jeffrey Skolnick
TOUCHSTONEX: protein structure prediction with sparse NMR data.
Proteins 2003;53(2):290-306.
2003: Yang Zhang; Andrzej Kolinski; Jeffrey Skolnick
TOUCHSTONE II: a new approach to ab initio protein structure prediction.
Biophysical journal 2003;85(2):1145-64.
2003: Andrzej Kolinski; Dominik Gront; Piotr Pokarowski; Jeffrey Skolnick
A simple lattice model that exhibits a protein-like cooperative all-or-none folding transition.
Biopolymers 2003;69(3):399-405.
2003: Piotr Pokarowski; Andrzej Kolinski; Jeffrey Skolnick
A minimal physically realistic protein-like lattice model: designing an energy landscape that ensures all-or-none folding to a unique native state.
Biophysical journal 2003;84(3):1518-26.
2003: Jeffrey Skolnick; Yang Zhang; Adrian Arakaki; Andrzej Kolinski; Michal Boniecki; András Szilágyi; Daisuke Kihara
TOUCHSTONE: a unified approach to protein structure prediction.
Proteins 2003;53 Suppl 6():469-79.
2002: Jorge Viñals; Andrzej Kolinski; Jeffrey Skolnick
Numerical study of the entropy loss of dimerization and the folding thermodynamics of the GCN4 leucine zipper.
Biophysical journal 2002;83(5):2801-11.
2002: Rafal R Sicinski; Piotr Rotkiewicz; Andrzej Kolinski; Wanda Sicinska; Jean M Prahl; Connie M Smith; Hector F Deluca
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.
Journal of medicinal chemistry 2002;45(16):3366-80.
2002: Daisuke Kihara; Yang Zhang; Hui Lu; Andrzej Kolinski; Jeffrey Skolnick
Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genome.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(9):5993-8.
2002: Andrzej Sikorski; Andrzej Kolinski; Jeffrey Skolnick
Computer simulations of protein folding with a small number of distance restraints.
Acta biochimica Polonica 2002;49(3):683-92.
2001: Janusz Bujnicki; Piotr Rotkiewicz; Andrzej Kolinski; Leszek Rychlewski
Three-dimensional modeling of the I-TevI homing endonuclease catalytic domain, a GIY-YIG superfamily member, using NMR restraints and Monte Carlo dynamics.
Protein engineering 2001;14(10):717-21.
2001: Daisuke Kihara; Hui Lu; Andrzej Kolinski; Jeffrey Skolnick
TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(18):10125-30.
2001: Piotr Rotkiewicz; Wanda Sicinska; Andrzej Kolinski; Hector F Deluca
Model of three-dimensional structure of vitamin D receptor and its binding mechanism with 1alpha,25-dihydroxyvitamin D(3).
Proteins 2001;44(3):188-99.
2001: Andrzej Kolinski; M R Betancourt; Daisuke Kihara; Piotr Rotkiewicz; Jeffrey Skolnick
Generalized comparative modeling (GENECOMP): a combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement.
Proteins 2001;44(2):133-49.
2001: Jeffrey Skolnick; Andrzej Kolinski; Daisuke Kihara; M Betancourt; Piotr Rotkiewicz; Michal Boniecki
Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement.
Proteins 2001;Suppl 5():149-56.
2000: Andrzej Sikorski; Andrzej Kolinski; Jeffrey Skolnick
Monte Carlo simulation of designed helical proteins.
Acta poloniae pharmaceutica 2000;57 Suppl():119-21.
2000: Michael Feig; Piotr Rotkiewicz; Andrzej Kolinski; Jeffrey Skolnick; Charles L Brooks
Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models.
Proteins 2000;41(1):86-97.
2000: A Sikorski; Andrzej Kolinski; Jeffrey Skolnick
Computer simulations of the properties of the alpha2, alpha2C, and alpha2D de novo designed helical proteins.
Proteins 2000;38(1):17-28.
1999: Andrzej Kolinski; Piotr Rotkiewicz; B Ilkowski; Jeffrey Skolnick
A method for the improvement of threading-based protein models.
Proteins 1999;37(4):592-610.
1999: Andrzej Kolinski; B Ilkowski; Jeffrey Skolnick
Dynamics and thermodynamics of beta-hairpin assembly: insights from various simulation techniques.
Biophysical journal 1999;77(6):2942-52.
1999: DEBASISA MOHANTY; Andrzej Kolinski; Jeffrey Skolnick
De novo simulations of the folding thermodynamics of the GCN4 leucine zipper.
Biophysical journal 1999;77(1):54-69.
1999: DEBASISA MOHANTY; Brian Dominy; Andrzej Kolinski; Charles L Brooks; Jeffrey Skolnick
Correlation between knowledge-based and detailed atomic potentials: application to the unfolding of the GCN4 leucine zipper.
Proteins 1999;35(4):447-52.
1999: AR Ortiz; Andrzej Kolinski; Piotr Rotkiewicz; B Ilkowski; Jeffrey Skolnick
Ab initio folding of proteins using restraints derived from evolutionary information.
Proteins 1999;Suppl 3():177-85.
1998: Jeffrey Skolnick; Andrzej Kolinski; AR Ortiz
Reduced protein models and their application to the protein folding problem.
Journal of biomolecular structure & dynamics 1998;16(2):381-96.
1998: Andrzej Kolinski; Jeffrey Skolnick
Assembly of protein structure from sparse experimental data: an efficient Monte Carlo model.
Proteins 1998;32(4):475-94.
1998: A Sikorski; Andrzej Kolinski; Jeffrey Skolnick
Computer simulations of de novo designed helical proteins.
Biophysical journal 1998;75(1):92-105.
1998: AR Ortiz; Andrzej Kolinski; Jeffrey Skolnick
Fold assembly of small proteins using monte carlo simulations driven by restraints derived from multiple sequence alignments.
Journal of molecular biology 1998;277(2):419-48.
1998: AR Ortiz; Andrzej Kolinski; Jeffrey Skolnick
Tertiary structure prediction of the KIX domain of CBP using Monte Carlo simulations driven by restraints derived from multiple sequence alignments.
Proteins 1998;30(3):287-94.
1998: AR Ortiz; Andrzej Kolinski; Jeffrey Skolnick
Nativelike topology assembly of small proteins using predicted restraints in Monte Carlo folding simulations.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(3):1020-5.
1998: AR Ortiz; Andrzej Kolinski; Jeffrey Skolnick
Combined multiple sequence reduced protein model approach to predict the tertiary structure of small proteins.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 1998;():377-88.
1997: WP Hu; Andrzej Kolinski; Jeffrey Skolnick
Improved method for prediction of protein backbone U-turn positions and major secondary structural elements between U-turns.
Proteins 1997;29(4):443-60.
1997: Andrzej Kolinski; Jeffrey Skolnick; A Godzik; WP Hu
A method for the prediction of surface "U"-turns and transglobular connections in small proteins.
Proteins 1997;27(2):290-308.
1997: Jeffrey Skolnick; Andrzej Kolinski; AR Ortiz
MONSSTER: a method for folding globular proteins with a small number of distance restraints.
Journal of molecular biology 1997;265(2):217-41.
1997: AR Ortiz; WP Hu; Andrzej Kolinski; Jeffrey Skolnick
Method for low resolution prediction of small protein tertiary structure.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 1997;():316-27.
1996: Andrzej Kolinski; W Galazka; Jeffrey Skolnick
On the origin of the cooperativity of protein folding: implications from model simulations.
Proteins 1996;26(3):271-87.
1996: K A Olszewski; Andrzej Kolinski; Jeffrey Skolnick
Folding simulations and computer redesign of protein A three-helix bundle motifs.
Proteins 1996;25(3):286-99.
1996: M Vieth; Andrzej Kolinski; Jeffrey Skolnick
Method for predicting the state of association of discretized protein models. Application to leucine zippers.
Biochemistry 1996;35(3):955-67.
1996: M Vieth; Andrzej Kolinski; Charles L Brooks; Jeffrey Skolnick
Prediction of the quaternary structure of coiled coils: GCN4 leucine zipper and its mutants.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 1996;():653-62.
1996: Andrzej Kolinski; Jeffrey Skolnick; Adam Godzik
An algorithm for prediction of structural elements in small proteins.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 1996;():446-60.
1996: K A Olszewski; Andrzej Kolinski; Jeffrey Skolnick
Does a backwardly read protein sequence have a unique native state?
Protein engineering 1996;9(1):5-14.
1995: M Vieth; Andrzej Kolinski; Charles L Brooks; Jeffrey Skolnick
Prediction of quaternary structure of coiled coils. Application to mutants of the GCN4 leucine zipper.
Journal of molecular biology 1995;251(3):448-67.
1994: M Vieth; Andrzej Kolinski; Charles L Brooks; Jeffrey Skolnick
Prediction of the folding pathways and structure of the GCN4 leucine zipper.
Journal of molecular biology 1994;237(4):361-7.
1994: Andrzej Kolinski; Jeffrey Skolnick
Monte Carlo simulations of protein folding. II. Application to protein A, ROP, and crambin.
Proteins 1994;18(4):353-66.
1994: Andrzej Kolinski; Jeffrey Skolnick
Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme.
Proteins 1994;18(4):338-52.
1993: Adam Godzik; Jeffrey Skolnick; Andrzej Kolinski
Regularities in interaction patterns of globular proteins.
Protein engineering 1993;6(8):801-10.
1993: Adam Godzik; Andrzej Kolinski; Jeffrey Skolnick
De novo and inverse folding predictions of protein structure and dynamics.
Journal of computer-aided molecular design 1993;7(4):397-438.
1993: Jeffrey Skolnick; Andrzej Kolinski; C L Brooks; Adam Godzik; A Rey
A method for predicting protein structure from sequence.
Current biology : CB 1993;3(7):414-23.
1993: Jeffrey Skolnick; Andrzej Kolinski; Adam Godzik
From independent modules to molten globules: observations on the nature of protein folding intermediates.
Proceedings of the National Academy of Sciences of the United States of America 1993;90(6):2099-100.
1992: Adam Godzik; Andrzej Kolinski; Jeffrey Skolnick
Topology fingerprint approach to the inverse protein folding problem.
Journal of molecular biology 1992;227(1):227-38.
1992: Adam Godzik; Jeffrey Skolnick; Andrzej Kolinski
Simulations of the folding pathway of triose phosphate isomerase-type alpha/beta barrel proteins.
Proceedings of the National Academy of Sciences of the United States of America 1992;89(7):2629-33.