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1

Calculation of protein conformation by global optimization of a potential energy function

Jooyoung Lee, Adam Liwo, Daniel R. Ripoll, Jaroslaw Pillardy, Harold A. Scheraga

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 235 KB

english, 1999

2

Hierarchical energy-based approach to protein-structure prediction: Blind-test evaluation with CASP3 targets

Jooyoung Lee, Adam Liwo, Daniel R. Ripoll, Jaroslaw Pillardy, Jeffrey A. Saunders, Kenneth D. Gibson, Harold A. Scheraga

Journal:

International Journal of Quantum Chemistry

Year:

2000

Language:

english

File:

PDF, 3.03 MB

english, 2000

3

Conformation-Family Monte Carlo (CFMC): An Efficient Computational Method for Identifying the Low-Energy States of a Macromolecule

Jaroslaw Pillardy, Cezary Czaplewski, William J. Wedemeyer, Harold A. Scheraga

Journal:

Helvetica Chimica Acta

Year:

2000

Language:

english

File:

PDF, 531 KB

english, 2000

4

ChemInform Abstract: Conformation-Family Monte Carlo (CFMC): An Efficient Computational Method for Identifying the Low-Energy States of a Macromolecule.

Jaroslaw Pillardy, Cezary Czaplewski, William J. Wedemeyer, Harold A. Scheraga

Journal:

Year:

2000

File:

PDF, 26 KB

2000

5

Evolution of physics-based methodology for exploring the conformational energy landscape of proteins

Harold A. Scheraga, Jaroslaw Pillardy, Adam Liwo, Jooyoung Lee, Cezary Czaplewski, Daniel R. Ripoll, William J. Wedemeyer, Yelena A. Arnautova

Journal:

Journal of Computational Chemistry

Year:

2002

Language:

english

File:

PDF, 111 KB

english, 2002

6

Theoretically predicted lowest-energy structures of water clusters

Jarosław Pillardy, Krzysztof A. Olszewski, Lucjan Piela

Journal:

Journal of Molecular Structure

Year:

1992

Language:

english

File:

PDF, 746 KB

english, 1992

7

Improved conformational space annealing method to treat β-structure with the UNRES force-field and to enhance scalability of parallel implementation

Cezary Czaplewski, Adam Liwo, Jarosław Pillardy, Stanisław Ołdziej, Harold A. Scheraga

Journal:

Year:

2004

Language:

english

File:

PDF, 662 KB

english, 2004

8

Enriching the sequence substitution matrix by structural information

Octavian Teodorescu, Tamara Galor, Jaroslaw Pillardy, Ron Elber

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 129 KB

english, 2004

9

A template-finding algorithm and a comprehensive benchmark for homology modeling of proteins

Brinda Kizhakke Vallat, Jaroslaw Pillardy, Ron Elber

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 697 KB

english, 2008

10

Building and assessing atomic models of proteins from structural templates: Learning and benchmarks

Brinda Kizhakke Vallat, Jaroslaw Pillardy, Peter Májek, Jaroslaw Meller, Thomas Blom, BaoQiang Cao, Ron Elber

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2009

Language:

english

File:

PDF, 324 KB

english, 2009

11

Prediction of protein structure using a knowledge-based off-lattice united-residue force field and global optimization methods

Adam Liwo, Jarosław Pillardy, Rajmund Kaźmierkiewicz, Ryszard J. Wawak, Małgorzata Groth, Cezary Czaplewski, Stanisaw Ołdziej, Harold A. Scheraga

Journal:

Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)

Year:

1999

Language:

english

File:

PDF, 283 KB

english, 1999

12

Surmounting the Multiple-Minima Problem in Protein Folding

Harold A. Scheraga, Jooyoung Lee, Jarosław Pillardy, Yuan-Jie Ye, Adam Liwo, Daniel Ripoll

Journal:

Journal of Global Optimization

Year:

1999

Language:

english

File:

PDF, 177 KB

english, 1999

13

Global Optimization-Based Method for Deriving Intermolecular Potential Parameters for Crystals

Arnautova, Yelena A., Pillardy, Jaroslaw, Czaplewski, Cezary, Scheraga, Harold A.

Journal:

Journal of Physical Chemistry B

Year:

2003

Language:

english

File:

PDF, 294 KB

english, 2003

14

Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field

Liwo, Adam, Czaplewski, Cezary, Pillardy, Jarosław, Scheraga, Harold A.

Journal:

The Journal of Chemical Physics

Year:

2001

Language:

english

File:

PDF, 1.29 MB

english, 2001

15

Protein Structure Prediction by Global Optimization of a Potential Energy Function

Adam Liwo, Jooyoung Lee, Daniel R. Ripoll, Jaroslaw Pillardy and Harold A. Scheraga

Journal:

Proceedings of the National Academy of Sciences

Year:

1999

Language:

english

File:

PDF, 998 KB

english, 1999

16

The transcriptome landscape of early maize meiosis

Dukowic-Schulze, Stefanie, Sundararajan, Anitha, Mudge, Joann, Ramaraj, Thiruvarangan, Farmer, Andrew D, Wang, Minghui, Sun, Qi, Pillardy, Jaroslaw, Kianian, Shahryar, Retzel, Ernest F, Pawlowski, Woj

Journal:

BMC Plant Biology

Year:

2014

Language:

english

File:

PDF, 894 KB

english, 2014

17

Crystal Structure Prediction by Global Optimization as a Tool for Evaluating Potentials: Role of the Dipole Moment Correction Term in Successful Predictions †

Pillardy, Jaroslaw, Wawak, Ryszard J., Arnautova, Yelena A., Czaplewski, Cezary, Scheraga, Harold A.

Journal:

Journal of the American Chemical Society

Year:

2000

Language:

english

File:

PDF, 319 KB

english, 2000

18

An Efficient Deformation-Based Global Optimization Method (Self-Consistent Basin-to-Deformed-Basin Mapping (SCBDBM)). Application to Lennard-Jones Atomic Clusters

Pillardy, Jarosław, Liwo, Adam, Scheraga, Harold A.

Journal:

Journal of Physical Chemistry A

Year:

1999

Language:

english

File:

PDF, 163 KB

english, 1999

19

Diffusion Equation and Distance Scaling Methods of Global Optimization: Applications to Crystal Structure Prediction

Wawak, Ryszard J., Pillardy, Jaroslaw, Liwo, Adam, Gibson, Kenneth D., Scheraga, Harold A.

Journal:

Journal of Physical Chemistry A

Year:

1998

Language:

english

File:

PDF, 165 KB

english, 1998

20

Reply to “Comment on ‘Crystal Structure Prediction by Global Optimization as a Tool for Evaluating Potentials: Role of the Dipole Moment Correction Term in Successful Predictions'” by B. P. van Eijck and J. Kroon

Wedemeyer, William J., Arnautova, Yelena A., Pillardy, Jaroslaw, Wawak, Ryszard J., Czaplewski, Cezary, Scheraga, Harold A.

Journal:

Journal of Physical Chemistry B

Year:

2000

Language:

english

File:

PDF, 27 KB

english, 2000

21

Development of Physics-Based Energy Functions that Predict Medium-Resolution Structures for Proteins of the α, β, and α/β Structural Classes

Pillardy, Jarosław, Czaplewski, Cezary, Liwo, Adam, Wedemeyer, William J., Lee, Jooyoung, Ripoll, Daniel R., Arłukowicz, Piotr, Ołdziej, Stanisław, Arnautova, Yelena A., Scheraga, Harold A.

Journal:

Journal of Physical Chemistry B

Year:

2001

Language:

english

File:

PDF, 480 KB

english, 2001

22

An Efficient Deformation-Based Global Optimization Method for Off-Lattice Polymer Chains: Self-Consistent Basin-to-Deformed-Basin Mapping (SCBDBM). Application to United-Residue Polypeptide Chains

Pillardy, Jaroslaw, Liwo, Adam, Groth, Malgorzata, Scheraga, Harold A.

Journal:

Journal of Physical Chemistry B

Year:

1999

Language:

english

File:

PDF, 194 KB

english, 1999

23

Derivation of a New Force Field for Crystal-Structure Prediction Using Global Optimization: Nonbonded Potential Parameters for Hydrocarbons and Alcohols

Arnautova, Yelena A., Jagielska, Anna, Pillardy, Jaroslaw, Scheraga, Harold A.

Journal:

Journal of Physical Chemistry B

Year:

2003

Language:

english

File:

PDF, 184 KB

english, 2003

24

Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 2. Off-Lattice Tests of the Method with Single Proteins

Ołdziej, Stanisław, Liwo, Adam, Czaplewski, Cezary, Pillardy, Jarosław, Scheraga, Harold A.

Journal:

Journal of Physical Chemistry B

Year:

2004

Language:

english

File:

PDF, 280 KB

english, 2004

25

Optimization of Parameters in Macromolecular Potential Energy Functions by Conformational Space Annealing

Lee, Jooyoung, Ripoll, Daniel R., Czaplewski, Cezary, Pillardy, Jarosław, Wedemeyer, William J., Scheraga, Harold A.

Journal:

Journal of Physical Chemistry B

Year:

2001

Language:

english

File:

PDF, 93 KB

english, 2001

26

Support Vector Training of Protein Alignment Models

Yu, Chun-Nam John, Joachims, Thorsten, Elber, Ron, Pillardy, Jaroslaw

Journal:

Journal of Computational Biology

Year:

2008

Language:

english

File:

PDF, 161 KB

english, 2008

27

Fast Geometric Consensus Approach for Protein Model Quality Assessment

Adamczak, Rafal, Pillardy, Jaroslaw, Vallat, Brinda K., Meller, Jaroslaw

Journal:

Journal of Computational Biology

Year:

2011

Language:

english

File:

PDF, 273 KB

english, 2011

28

Molecular Dynamics on Deformed Potential Energy Hypersurfaces

Pillardy, Jaroslaw, Piela, Lucjan

Journal:

Journal of Physical Chemistry

Year:

1995

Language:

english

File:

PDF, 891 KB

english, 1995

29

Performance of the shift method of global minimization in searches for optimum structures of clusters of Lennard-Jones atoms

Pillardy, Jaroslaw, Olszewski, Krzysztof A., Piela, Lucjan

Journal:

Journal of Physical Chemistry

Year:

1992

Language:

english

File:

PDF, 608 KB

english, 1992

30

[ACM Press the fourth annual international conference - Tokyo, Japan (2000..-..)] Proceedings of the fourth annual international conference on Computational molecular biology - RECOMB '00 - UNRES

Liwo, Adam, Oldziej, Stanislaw, Scheraga, Harold A., Pillardy, Jaroslaw, Czaplewski, Cezary, Lee, Jooyoung, Ripoll, Daniel R., Groth, Malgorzata, Rodziewicz-Motowidlo, Sylwia, Kamierkiewicz, Rajmund,

Year:

2000

Language:

english

File:

PDF, 585 KB

english, 2000

31

Fibrosis Progression in Patients with Chronic Hepatitis C Virus Infection

Zeremski, Marija, Dimova, Rositsa B., Pillardy, Jaroslaw, de Jong, Ype P., Jacobson, Ira M., Talal, Andrew H.

Journal:

The Journal of Infectious Diseases

Year:

2016

Language:

english

File:

PDF, 1.55 MB

english, 2016

32

Correction to: The transcriptome landscape of early maize meiosis

Dukowic-Schulze, Stefanie, Sundararajan, Anitha, Mudge, Joann, Ramaraj, Thiruvarangan, Farmer, Andrew D., Wang, Minghui, Sun, Qi, Pillardy, Jaroslaw, Kianian, Shahryar, Retzel, Ernest F., Pawlowski, W

Journal:

BMC Plant Biology

Year:

2018

Language:

english

File:

PDF, 443 KB

english, 2018

33

High-resolution crossover mapping reveals similarities and differences of male and female recombination in maize

Kianian, Penny M. A., Wang, Minghui, Simons, Kristin, Ghavami, Farhad, He, Yan, Dukowic-Schulze, Stefanie, Sundararajan, Anitha, Sun, Qi, Pillardy, Jaroslaw, Mudge, Joann, Chen, Changbin, Kianian, Sha

Journal:

Nature Communications

Year:

2018

Language:

english

File:

PDF, 875 KB

english, 2018