Volume 32; Issue 12

Journal of Computational Chemistry

Volume 32; Issue 12

1

Three-residue loop closure in proteins: A new kinematic method reveals a locus of connected loop conformations

Ali Nekouzadeh, Yoram Rudy

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 923 KB

english, 2011

2

Quantitative symmetry and chirality—A fast computational algorithm for large structures: Proteins, macromolecules, nanotubes, and unit cells

Chaim Dryzun, Amir Zait, David Avnir

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 1.06 MB

english, 2011

3

A novel graphical representation of protein sequences and its application

Bo Liao, Benyou Liao, Xinguo Lu, Zhi Cao

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 630 KB

english, 2011

4

Alkaline hydrolysis of ethylene phosphate: An ab initio study by supermolecule model and polarizable continuum approach

Futing Xia, Hua Zhu

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 461 KB

english, 2011

5

Theoretical study on the ring-opening isomerization reaction mechanism of the ring isomers of N8H8

Han-Ying Wu, Wan-Fei Cai, Lai-Cai Li, An-Min Tian, Ning-Bew Wong

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 1.48 MB

english, 2011

6

Molecular mechanical study of halogen bonding in drug discovery

Mahmoud A. A. Ibrahim

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 682 KB

english, 2011

7

PROCOS: Computational analysis of protein–protein complexes

Florian Fink, Jochen Hochrein, Vincent Wolowski, Rainer Merkl, Wolfram Gronwald

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 341 KB

english, 2011

8

Accurate assessment of the strain energy in a protein-bound drug using QM/MM X-ray refinement and converged quantum chemistry

Zheng Fu, Xue Li, Kenneth M. Merz Jr.

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 3.84 MB

english, 2011

9

SDOCK: A global protein-protein docking program using stepwise force-field potentials

Changsheng Zhang, Luhua Lai

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 1.12 MB

english, 2011

10

Water order profiles on phospholipid/cholesterol membrane bilayer surfaces

David Robinson, Nicholas A. Besley, Paul O'shea, Jonathan D. Hirst

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 246 KB

english, 2011

11

Single electron densities: A new tool to analyze molecular wavefunctions

Arne Lüchow, René Petz

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 214 KB

english, 2011

12

A chirality-based metrics for free-energy calculations in biomolecular systems

Adriana Pietropaolo, Davide Branduardi, Massimiliano Bonomi, Michele Parrinello

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 1.48 MB

english, 2011

13

Indexing molecules with chemical graph identifiers

Elisabet Gregori-Puigjané, Rut Garriga-Sust, Jordi Mestres

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 461 KB

english, 2011

14

Derivatives of molecular surface area and volume: Simple and exact analytical formulas

Konstantin V. Klenin, Frank Tristram, Timo Strunk, Wolfgang Wenzel

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 519 KB

english, 2011

15

Theoretical modulation of the color of light emitted by firefly oxyluciferin

Luís Pinto Da Silva, Joaquim C. G. Esteves Da Silva

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 296 KB

english, 2011

16

Combining a polarizable force-field and a coarse-grained polarizable solvent model. II. Accounting for hydrophobic effects

Michel Masella, Daniel Borgis, Philippe Cuniasse

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 763 KB

english, 2011

17

Brownian dynamics simulations on CPU and GPU with BD_BOX

Maciej Długosz, Paweł Zieliński, Joanna Trylska

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 400 KB

english, 2011

18

CORAL: Quantitative structure–activity relationship models for estimating toxicity of organic compounds in rats

A. P. Toropova, A. A. Toropov, E. Benfenati, G. Gini, D. Leszczynska, J. Leszczynski

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 400 KB

english, 2011

19

Nonideality in diffusion of ionic and neutral solutes and hydrogen bond dynamics in dimethyl sulfoxide–chloroform mixtures of varying composition

Rini Gupta, Amalendu Chandra

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 457 KB

english, 2011

20

Gradients for configuration interaction energies with spin-orbit coupling in a semiempirical framework

Giovanni Granucci, Maurizio Persico

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 182 KB

english, 2011

21

Stepwise disproportionation in polyelectrolyte complexes

R. S. Dias, P. Linse, A. A. C. C. Pais

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 559 KB

english, 2011

22

Theoretical study on the unimolecular decomposition of thiophenol

Ala'a H. Al-Muhtaseb, Mohammednoor Altarawneh, Mansour H. Almatarneh, Raymond A. Poirier, Niveen W. Assaf

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 567 KB

english, 2011

23

A computational study of unique properties of pillar[n]quinones: Self-assembly to tubular structures and potential applications as electron acceptors and anion recognizers

Ka-un Lao, Chin-hui Yu

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 468 KB

english, 2011