Andrzej, Kolinski: search on Z-Library

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1

Protein–peptide docking: opportunities and challenges

Ciemny, Maciej, Kurcinski, Mateusz, Kamel, Karol, Kolinski, Andrzej, Alam, Nawsad, Schueler-Furman, Ora, Kmiecik, Sebastian

Journal:

Drug Discovery Today

Year:

2018

Language:

english

File:

PDF, 852 KB

english, 2018

2

Protein fragment reconstruction using various modeling techniques

Michal Boniecki, Piotr Rotkiewicz, Jeffrey Skolnick, Andrzej Kolinski

Journal:

Journal of Computer-Aided Molecular Design

Year:

2003

Language:

english

File:

PDF, 398 KB

english, 2003

3

Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement

Jeffrey Skolnick, Andrzej Kolinski, Daisuke Kihara, Marcos Betancourt, Piotr Rotkiewicz, Michal Boniecki

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2001

Language:

english

File:

PDF, 550 KB

english, 2001

4

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

Kurcinski, Mateusz, Kolinski, Andrzej, Kmiecik, Sebastian

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 1.77 MB

english, 2014

5

Coarse-Grained Protein Models and Their Applications

Kmiecik, Sebastian, Gront, Dominik, Kolinski, Michal, Wieteska, Lukasz, Dawid, Aleksandra Elzbieta, Kolinski, Andrzej

Journal:

Chemical Reviews

Year:

2016

Language:

english

File:

PDF, 6.26 MB

english, 2016

6

Algorithm for rapid reconstruction of protein backbone from alpha carbon coordinates

Milik, Mariusz, Kolinski, Andrzej, Skolnick, Jeffrey

Journal:

Journal of Computational Chemistry

Year:

1997

Language:

english

File:

PDF, 244 KB

english, 1997

7

Assessing energy functions for flexible docking

Vieth, Michal, Hirst, Jonathan D., Kolinski, Andrzej, Brooks, Charles L.

Journal:

Journal of Computational Chemistry

Year:

1998

Language:

english

File:

PDF, 302 KB

english, 1998

8

Folding simulations and computer redesign of protein A three-helix bundle motifs

Krzysztof A. Olszewski, Andrzej Kolinski, Jeffrey Skolnick

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1996

Language:

english

File:

PDF, 1.50 MB

english, 1996

9

On the origin of the cooperativity of protein folding: Implications from model simulations

Kolinski, Andrzej, Galazka, Wojciech, Skolnick, Jeffrey

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1996

Language:

english

File:

PDF, 1.46 MB

english, 1996

10

A method for the prediction of surface “U”-turns and transglobular connections in small proteins

Andrzej Kolinski, Jeffrey Skolnick, Adam Godzik, Wei-Ping Hu

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1997

Language:

english

File:

PDF, 341 KB

english, 1997

11

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

Wei-Ping Hu, Andrzej Kolinski, Jeffrey Skolnick

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1997

Language:

english

File:

PDF, 257 KB

english, 1997

12

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

Angel R. Ortiz, Andrzej Kolinski, Jeffrey Skolnick

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1998

Language:

english

File:

PDF, 274 KB

english, 1998

13

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

Andrzej Kolinski, Jeffrey Skolnick

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1998

Language:

english

File:

PDF, 302 KB

english, 1998

14

Ab initio folding of proteins using restraints derived from evolutionary information

Angel R. Ortiz, Andrzej Kolinski, Piotr Rotkiewicz, Bartosz Ilkowski, Jeffrey Skolnick

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 432 KB

english, 1999

15

Correlation between knowledge-based and detailed atomic potentials: Application to the unfolding of the GCN4 leucine zipper

Debasisa Mohanty, Brian N. Dominy, Andrzej Kolinski, Charles L. Brooks III, Jeffrey Skolnick

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 107 KB

english, 1999

16

A method for the improvement of threading-based protein models

Andrzej Kolinski, Piotr Rotkiewicz, Bartosz Ilkowski, Jeffrey Skolnick

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 627 KB

english, 1999

17

Derivation of protein-specific pair potentials based on weak sequence fragment similarity

Jeffrey Skolnick, Andrzej Kolinski, Angel Ortiz

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2000

Language:

english

File:

PDF, 156 KB

english, 2000

18

Computer simulations of the properties of the α2, α2C, and α2D de novo designed helical proteins

Andrzej Sikorski, Andrzej Kolinski, Jeffrey Skolnick

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2000

Language:

english

File:

PDF, 286 KB

english, 2000

19

Collapse transitions in protein-like lattice polymers: The effect of sequence patterns

Andrzej Kolinski, Pawel Madziar

Journal:

Year:

1997

Language:

english

File:

PDF, 138 KB

english, 1997

20

De novo predictions of the quaternary structure of leucine zippers and other coiled coils

Jeffrey Skolnick, Andrzej Kolinski, Debasisa Mohanty

Journal:

International Journal of Quantum Chemistry

Year:

1999

Language:

english

File:

PDF, 200 KB

english, 1999

21

Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models

Michael Feig, Piotr Rotkiewicz, Andrzej Kolinski, Jeffrey Skolnick, Charles L. Brooks III

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2000

Language:

english

File:

PDF, 305 KB

english, 2000

22

Helix-coil and beta sheet-coil transitions in a simplified, yet realistic protein model

Bartosz Ilkowski, Jeffrey Skolnick, Andrzej Kolinski

Journal:

Macromolecular Theory and Simulations

Year:

2000

Language:

english

File:

PDF, 207 KB

english, 2000

23

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

Andrzej Kolinski, Dominik Gront, Piotr Pokarowski, Jeffrey Skolnick

Journal:

Year:

2003

Language:

english

File:

PDF, 180 KB

english, 2003

24

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

Turkan Haliloglu, Andrzej Kolinski, Jeffrey Skolnick

Journal:

Year:

2003

Language:

english

File:

PDF, 1.74 MB

english, 2003

25

Monte carlo studies on equilibrium globular protein folding. I. Homopolymeric lattice models of β-barrel proteins

Andrzej Kolinski, Jeffrey Skolnick, Robert Yaris

Journal:

Year:

1987

Language:

english

File:

PDF, 1.26 MB

english, 1987

26

Monte carlo studies on equilibrium globular protein folding. II. β-barrel globular protein models

Jeffrey Skolnick, Andrzej Kolinski, Robert Yaris

Journal:

Year:

1989

Language:

english

File:

PDF, 1.81 MB

english, 1989

27

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

Dominik Gront, Sebastian Kmiecik, Andrzej Kolinski

Journal:

Journal of Computational Chemistry

Year:

2007

Language:

english

File:

PDF, 138 KB

english, 2007

28

Protein structure prediction: Combining de novo modeling with sparse experimental data

Dorota Latek, Dariusz Ekonomiuk, Andrzej Kolinski

Journal:

Journal of Computational Chemistry

Year:

2007

Language:

english

File:

PDF, 357 KB

english, 2007

29

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

Dorota Latek, Andrzej Kolinski

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 903 KB

english, 2011

30

Lattice representations of globular proteins: How good are they?

Adam Godzik, Andrzej Kolinski, Jeffrey Skolnick

Journal:

Journal of Computational Chemistry

Year:

1993

Language:

english

File:

PDF, 781 KB

english, 1993

31

Dynamics of star branched polymers in a matrix of linear chains — a Monte Carlo study

Andrzej Sikorski, Andrzej Kolinski, Jeffrey Skolnick

Journal:

Macromolecular Theory and Simulations

Year:

1994

Language:

english

File:

PDF, 781 KB

english, 1994

32

Protein Folding with a Reduced Model and Inaccurate Short-Range Restraints

Dorota Plewczynska, Andrzej Kolinski

Journal:

Macromolecular Theory and Simulations

Year:

2005

Language:

english

File:

PDF, 311 KB

english, 2005

33

Some properties of rigid cores with flexible tails. Monte carlo simulation of two-dimensional lattice systems

Andrzej Koliński

Journal:

Chemical Physics Letters

Year:

1985

Language:

english

File:

PDF, 373 KB

english, 1985

34

Computer modelling of radiation-induced in-source solid state polymerizations

Andrzej Országh, Andrzej Koliński, Piotr Romiszowski

Journal:

Year:

1979

Language:

english

File:

PDF, 204 KB

english, 1979

35

Monte Carlo simulation of radiation-induced solid state polymerization

Piotr Romiszowski, Andrzej Kolinski

Journal:

Year:

1982

Language:

english

File:

PDF, 379 KB

english, 1982

36

Modeling of loops in proteins: a multi-method approach

Michal Jamroz, Andrzej Kolinski

Journal:

BMC Structural Biology

Year:

2010

Language:

english

File:

PDF, 1.95 MB

english, 2010

37

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

Sebastian Kmiecik, Dominik Gront, Andrzej Kolinski

Journal:

BMC Structural Biology

Year:

2007

Language:

english

File:

PDF, 5.48 MB

english, 2007

38

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

Elena M Ibryashkina, Marina V Zakharova, Vladimir B Baskunov, Ekaterina S Bogdanova, Maxim O Nagornykh, Marat M Den'mukhamedov, Bogdan S Melnik, Andrzej Kolinski, Dominik Gront, Marcin Feder, Alexande

Journal:

BMC Structural Biology

Year:

2007

Language:

english

File:

PDF, 1.34 MB

english, 2007

39

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

Dorota Latek, Andrzej Kolinski

Journal:

BMC Structural Biology

Year:

2008

Language:

english

File:

PDF, 1.25 MB

english, 2008

40

Monte carlo calculations of the ⊝ point of star-branched macromolecules on tetrahedral lattice

Andrzej Koliński, Andrzej Sikorski

Journal:

Journal of Polymer Science Part C: Polymer Letters

Year:

1982

Language:

english

File:

PDF, 179 KB

english, 1982

41

Monte Carlo study of star-branched polymers on the tetrahedral lattice. I. Conformation of the macromolecule

Andrzej Kolinski, Andrzej Sikorski

Journal:

Journal of Polymer Science Part A: Polymer Chemistry

Year:

1982

Language:

english

File:

PDF, 422 KB

english, 1982

42

On the entropy of the multichain athermal lattice systems

Andrzej Kolinski

Journal:

Journal of Polymer Science Part C: Polymer Letters

Year:

1984

Language:

english

File:

PDF, 186 KB

english, 1984

43

Monte carlo study of star-branched polymers on the tetrahedral lattice. II. Statistical thermodynamics of single macromolecules

Andrzej Sikorski, Andrzej Koliński

Journal:

Journal of Polymer Science Part A: Polymer Chemistry

Year:

1984

Language:

english

File:

PDF, 528 KB

english, 1984

44

Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets

Adam Godzik, Jeffrey Skolnick, Andrzej Koliński

Journal:

Protein Science

Year:

1995

Language:

english

File:

PDF, 1.14 MB

english, 1995

45

TOUCHSTONEX: Protein structure prediction with sparse NMR data

Wei Li, Yang Zhang, Daisuke Kihara, Yuanpeng Janet Huang, Deyou Zheng, Gaetano T. Montelione, Andrzej Kolinski, Jeffrey Skolnick

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2003

Language:

english

File:

PDF, 343 KB

english, 2003

46

TOUCHSTONE: A unified approach to protein structure prediction

Jeffrey Skolnick, Yang Zhang, Adrian K. Arakaki, Andrzej Kolinski, Michal Boniecki, András Szilágyi, Daisuke Kihara

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2003

Language:

english

File:

PDF, 753 KB

english, 2003

47

Model of three-dimensional structure of vitamin D receptor and its binding mechanism with 1α,25-dihydroxyvitamin D3

Piotr Rotkiewicz, Wanda Sicinska, Andrzej Kolinski, Hector F. DeLuca

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2001

Language:

english

File:

PDF, 594 KB

english, 2001

48

Inferring ideal amino acid interaction forms from statistical protein contact potentials

Piotr Pokarowski, Andrzej Kloczkowski, Robert L. Jernigan, Neha S. Kothari, Maria Pokarowska, Andrzej Kolinski

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 1.12 MB

english, 2005

49

Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models

Andrzej Koliński, Janusz M. Bujnicki

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 988 KB

english, 2005

50

Ideal amino acid exchange forms for approximating substitution matrices

Piotr Pokarowski, Andrzej Kloczkowski, Szymon Nowakowski, Maria Pokarowska, Robert L. Jernigan, Andrzej Kolinski

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2007

Language:

english

File:

PDF, 4.52 MB

english, 2007