Volume 82; Issue 9

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Proteins: Structure, Function, and Bioinformatics
Volume 82; Issue 9

Proteins: Structure, Function, and Bioinformatics

Volume 82; Issue 9

1

Helix kinks are equally prevalent in soluble and membrane proteins

Wilman, Henry R., Shi, Jiye, Deane, Charlotte M.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 4.28 MB

english, 2014

2

WeFold: A coopetition for protein structure prediction

Khoury, George A., Liwo, Adam, Khatib, Firas, Zhou, Hongyi, Chopra, Gaurav, Bacardit, Jaume, Bortot, Leandro O., Faccioli, Rodrigo A., Deng, Xin, He, Yi, Krupa, Pawel, Li, Jilong, Mozolewska, Magdalen

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 2.60 MB

english, 2014

3

Feature selection and classification of protein-protein complexes based on their binding affinities using machine learning approaches

Yugandhar, K., Gromiha, M. Michael

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 777 KB

english, 2014

4

Structural and sequence features of two residue turns in beta-hairpins

Madan, Bharat, Seo, Sung Yong, Lee, Sun-Gu

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 523 KB

english, 2014

5

Structure-guided approach for detecting large domain inserts in protein sequences as illustrated using the haloacid dehalogenase superfamily

Pandya, Chetanya, Dunaway-Mariano, Debra, Xia, Yu, Allen, Karen N.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 1.72 MB

english, 2014

6

Cofactory: Sequence-based prediction of cofactor specificity of Rossmann folds

Geertz-Hansen, Henrik Marcus, Blom, Nikolaj, Feist, Adam M., Brunak, Søren, Petersen, Thomas Nordahl

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 306 KB

english, 2014

7

Cation-π, amino-π, π-π, and H-bond interactions stabilize antigen-antibody interfaces

Dalkas, Georgios A., Teheux, Fabian, Kwasigroch, Jean Marc, Rooman, Marianne

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 409 KB

english, 2014

8

Improving fragment quality for de novo structure prediction

Shrestha, Rojan, Zhang, Kam Y. J.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 2.19 MB

english, 2014

9

A simple contact mapping algorithm for identifying potential peptide mimetics in protein-protein interaction partners

Krall, Alex, Brunn, Jonathan, Kankanala, Spandana, Peters, Michael H.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 1.64 MB

english, 2014

10

Essential function of the N-termini tails of the proteasome for the gating mechanism revealed by molecular dynamics simulations

Ishida, Hisashi

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 907 KB

english, 2014

11

Molecular dynamics simulation of the phosphorylation-induced conformational changes of a tau peptide fragment

Lyons, Albert J., Gandhi, Neha S., Mancera, Ricardo L.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 1.60 MB

english, 2014

12

Importance of polarization effect in the study of metalloproteins: Application of polarized protein specific charge scheme in predicting the reduction potential of azurin

Wei, Caiyi, Lazim, Raudah, Zhang, Dawei

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 422 KB

english, 2014

13

An amino acid code for β-sheet packing structure

Joo, Hyun, Tsai, Jerry

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 935 KB

english, 2014

14

An integrated approach for thermal stabilization of a mesophilic adenylate kinase

Moon, Sojin, Jung, Du-kyo, Phillips, George N., Bae, Euiyoung

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 800 KB

english, 2014

15

Structural and functional studies of a trans -acyltransferase polyketide assembly line enzyme that catalyzes stereoselective α- and β-ketoreduction

Piasecki, Shawn K., Zheng, Jianting, Axelrod, Abram J., E. Detelich, Madeline, Keatinge-Clay, Adrian T.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 891 KB

english, 2014

16

Assessment of protein side-chain conformation prediction methods in different residue environments

Peterson, Lenna X., Kang, Xuejiao, Kihara, Daisuke

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 827 KB

english, 2014

17

Kinetics of protein fibrillation controlled by fibril elongation

Kashchiev, Dimo

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 975 KB

english, 2014

18

Banding 2of NMR-derived methyl order parameters: Implications for protein dynamics

Sharp, Kim A., Kasinath, Vignesh, Wand, A. Joshua

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 489 KB

english, 2014

19

Crystal structure of JHP933 from Helicobacter pylori J99 shows two-domain architecture with a DUF1814 family nucleotidyltransferase domain and a helical bundle domain

Yoon, Ji Young, Lee, Sang Jae, Kim, Do Jin, Lee, Bong-Jin, Yang, Jin Kuk, Suh, Se Won

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 502 KB

english, 2014

20

Effects of protein engineering and rational mutagenesis on crystal lattice of single chain antibody fragments

Kalyoncu, Sibel, Hyun, Jeongmin, Pai, Jennifer C., Johnson, Jennifer L., Entzminger, Kevin, Jain, Avni, Heaner, David P., Morales, Ivan A., Truskett, Thomas M., Maynard, Jennifer A., Lieberman, Raquel

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 628 KB

english, 2014

21

Temperature and pressure effects on C112S azurin: Volume, expansivity, and flexibility changes

Cioni, Patrizia, Gabellieri, Edi, Marchal, Stéphane, Lange, Reinhard

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 619 KB

english, 2014

22

Homologous steroid receptors assemble at identical promoter architectures with unique energetics of cooperativity

Connaghan, Keith D., Yang, Qin, Miura, Michael T., Moody, Amie D., Bain, David L.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 477 KB

english, 2014

23

A critical survey of average distances between catalytic carboxyl groups in glycoside hydrolases

Mhlongo, Ndumiso N., Skelton, Adam A., Kruger, Gert, Soliman, Mahmoud E.S., Williams, Ian H.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 327 KB

english, 2014

24

ProDomAs, protein domain assignment algorithm using center-based clustering and independent dominating set

Ansari, Elnaz Saberi, Eslahchi, Changiz, Pezeshk, Hamid, Sadeghi, Mehdi

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 544 KB

english, 2014

25

Structural studies of bovine, equine, and leporine serum albumin complexes with naproxen

Bujacz, Anna, Zielinski, Kamil, Sekula, Bartosz

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 678 KB

english, 2014

26

Incorporating replacement free energy of binding-site waters in molecular docking

Sun, Hanzi, Zhao, Lifeng, Peng, Shiming, Huang, Niu

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 791 KB

english, 2014

27

Unbinding free energy of acetylcholinesterase bound oxime drugs along the gorge pathway from metadynamics-umbrella sampling investigation

Pathak, Arup K., Bandyopadhyay, Tusar

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 1.38 MB

english, 2014

28

Mode coupling points to functionally important residues in myosin II

Varol, Onur, Yuret, Deniz, Erman, Burak, Kabakçıoğlu, Alkan

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 918 KB

english, 2014

29

Structural conservation of the B subunit in the ammonia monooxygenase/particulate methane monooxygenase superfamily

Lawton, Thomas J., Ham, Jungwha, Sun, Tianlin, Rosenzweig, Amy C.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 479 KB

english, 2014

30

Influence of a heptad repeat stutter on the pH-dependent conformational behavior of the central coiled-coil from influenza hemagglutinin HA2

Higgins, Chelsea D., Malashkevich, Vladimir N., Almo, Steven C., Lai, Jonathan R.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 689 KB

english, 2014

31

Functional and structural studies of pullulanase from Anoxybacillus sp. LM18-11

Xu, Jianyong, Ren, Feifei, Huang, Chun-Hsiang, Zheng, Yingying, Zhen, Jie, Sun, Hong, Ko, Tzu-Ping, He, Miao, Chen, Chun-Chi, Chan, Hsiu-Chien, Guo, Rey-Ting, Song, Hui, Ma, Yanhe

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 691 KB

english, 2014

32

Crystal structure of a Chlamydomonas reinhardtii flagellar RabGAP TBC-domain at 1.8 Å resolution

Bhogaraju, Sagar, Lorentzen, Esben

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 544 KB

english, 2014

33

Substrate-mediated control of the conformation of an ancillary domain delivers a competent catalytic site for N -acetylneuraminic acid synthase

Joseph, Dmitri D. A., Jiao, Wanting, Kessans, Sarah A., Parker, Emily J.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 864 KB

english, 2014

34

Crystal structure of the Mycobacterium tuberculosis phosphate binding protein PstS3

Ferraris, Davide M., Spallek, Ralf, Oehlmann, Wulf, Singh, Mahavir, Rizzi, Menico

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 412 KB

english, 2014

35

Identification of the bona fide DHDPS from a common plant pathogen

Atkinson, Sarah C., Hor, Lilian, Dogovski, Con, Dobson, Renwick C. J., Perugini, Matthew A.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 779 KB

english, 2014

36

Multiple conformational states and gate opening of outer membrane protein TolC revealed by molecular dynamics simulations

Wang, Beibei, Weng, Jingwei, Wang, Wenning

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 714 KB

english, 2014

37

BetaVoid: Molecular voids via beta-complexes and Voronoi diagrams

Kim, Jae-Kwan, Cho, Youngsong, Laskowski, Roman A, Ryu, Seong Eon, Sugihara, Kokichi, Kim, Deok-Soo

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 1.85 MB

english, 2014

38

A novel TctA citrate transporter from an activated sludge metagenome: Structural and mechanistic predictions for the TTT family

Batista-García, Ramón Alberto, Sánchez-Reyes, Ayixon, Millán-Pacheco, César, González-Zuñiga, Víctor Manuel, Juárez, Soledad, Folch-Mallol, Jorge Luis, Pastor, Nina

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 660 KB

english, 2014

39

Rebuilding a macromolecular membrane complex at the atomic scale: Case of the Kir6.2 potassium channel coupled to the muscarinic acetylcholine receptor M2

Sapay, Nicolas, Estrada-Mondragon, Argel, Moreau, Christophe, Vivaudou, Michel, Crouzy, Serge

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 896 KB

english, 2014

40

Bridging between normal mode analysis and elastic network models

Na, Hyuntae, Song, Guang

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 266 KB

english, 2014

41

Crystal structure of phosphopantothenate synthetase from Thermococcus kodakarensis

Kishimoto, Asako, Kita, Akiko, Ishibashi, Takuya, Tomita, Hiroya, Yokooji, Yuusuke, Imanaka, Tadayuki, Atomi, Haruyuki, Miki, Kunio

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 1.39 MB

english, 2014

42

Exploring the multiscale signaling behavior of phototropin1 from Chlamydomonas reinhardtii using a full-residue space kinetic Monte Carlo molecular dynamics technique

Peter, Emanuel, Dick, Bernhard, Stambolic, Ivan, Baeurle, Stephan A.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 1.28 MB

english, 2014

43

Multiple Gaussian network modes alignment reveals dynamically variable regions: The hemoglobin case

Davis, Meir, Tobi, Dror

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 718 KB

english, 2014

44

Protein side-chain modeling with a protein-dependent optimized rotamer library

Francis-Lyon, Patricia, Koehl, Patrice

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 824 KB

english, 2014

45

Detecting protein atom correlations using correlation of probability of recurrence

Fataftah, Hiba, Karain, Wael

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 1.40 MB

english, 2014

46

The influenza fusion peptide promotes lipid polar head intrusion through hydrogen bonding with phosphates and N-terminal membrane insertion depth

Légaré, Sébastien, Lagüe, Patrick

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 529 KB

english, 2014

47

Crystal structure of DszC from Rhodococcus sp. XP at 1.79 Å

Liu, Shiheng, Zhang, Conggang, Su, Tiantian, Wei, Tiandi, Zhu, Deyu, Wang, Kang, Huang, Yan, Dong, Yuhui, Yin, Kun, Xu, Sujuan, Xu, Ping, Gu, Lichuan

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 1.68 MB

english, 2014

48

Comparative analysis of sequence covariation methods to mine evolutionary hubs: Examples from selected GPCR families

Pelé, Julien, Moreau, Matthieu, Abdi, Hervé, Rodien, Patrice, Castel, Hélène, Chabbert, Marie

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 901 KB

english, 2014

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