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1

Computational methods in drug discovery

Leelananda, Sumudu P, Lindert, Steffen

Journal:

Beilstein Journal of Organic Chemistry

Year:

2016

Language:

english

File:

PDF, 3.47 MB

english, 2016

2

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

Pawel Gniewek, Sumudu P. Leelananda, Andrzej Kolinski, Robert L. Jernigan, Andrzej Kloczkowski

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2011

Language:

english

File:

PDF, 788 KB

english, 2011

3

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

Michael T. Zimmermann, Sumudu P. Leelananda, Pawel Gniewek, Yaping Feng, Robert L. Jernigan, Andrzej Kloczkowski

Journal:

Journal of Structural and Functional Genomics

Year:

2011

Language:

english

File:

PDF, 471 KB

english, 2011

4

Incorporating Protein Topology Information in Similarity Matrices for Improved Sequence Matching (A Fold-Specific Scoring System)

Leelananda, Sumudu P., Jernigan, Robert L.

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 115 KB

english, 2013

5

Diversity of Sequences Folding to Highly and Poorly Designable Structures

Leelananda, Sumudu P., Jernigan, Robert L.

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 36 KB

english, 2012

6

Combining Statistical Potentials with Dynamics-Based Entropies Improves Selection from Protein Decoys and Docking Poses

Zimmermann, Michael T., Leelananda, Sumudu P., Kloczkowski, Andrzej, Jernigan, Robert L.

Journal:

Journal of Physical Chemistry B

Year:

2012

Language:

english

File:

PDF, 332 KB

english, 2012

7

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

Pawel, Gniewek, Leelananda, Sumudu P., Andrzej, Kolinski, Jernigan, Robert L., Andrzej, Kloczkowski

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 32 KB

english, 2014

8

The importance of slow motions for protein functional loops

Skliros, Aris, Zimmermann, Michael T, Chakraborty, Debkanta, Saraswathi, Saras, Katebi, Ataur R, Leelananda, Sumudu P, Kloczkowski, Andrzej, Jernigan, Robert L

Journal:

Physical Biology

Year:

2012

Language:

english

File:

PDF, 603 KB

english, 2012

9

Exploration of the relationship between topology and designability of conformations

Leelananda, Sumudu P., Towfic, Fadi, Jernigan, Robert L., Kloczkowski, Andrzej

Journal:

The Journal of Chemical Physics

Year:

2011

Language:

english

File:

PDF, 472 KB

english, 2011

10

Predicting Designability of Small Proteins from Graph Features of Contact Maps

Leelananda, Sumudu P., Jernigan, Robert L., Kloczkowski, Andrzej

Journal:

Journal of Computational Biology

Year:

2016

Language:

english

File:

PDF, 618 KB

english, 2016

11

Fold-specific sequence scoring improves protein sequence matching

Leelananda, Sumudu P., Kloczkowski, Andrzej, Jernigan, Robert L.

Journal:

BMC Bioinformatics

Year:

2016

Language:

english

File:

PDF, 1.03 MB

english, 2016

12

Iterative Molecular Dynamics−Rosetta Membrane Protein Structure Refinement Guided by Cryo-EM Densities

Leelananda, Sumudu, Lindert, Steffen

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 40 KB

english, 2018

13

Using NMR Chemical Shifts and Cryo-EM Density Restraints in Iterative Rosetta-MD Protein Structure Refinement

Leelananda, Sumudu P., Lindert, Steffen

Journal:

Journal of Chemical Information and Modeling

Year:

2019

Language:

english

File:

PDF, 4.82 MB

english, 2019

14

Using NMR Chemical Shifts and Cryo-EM Density Restraints in Iterative Rosetta-MD Protein Structure Refinement

Leelananda, Sumudu P., Lindert, Steffen

Journal:

Journal of Chemical Information and Modeling

Year:

2019

File:

PDF, 4.82 MB

2019

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