Works matching IS 08873585 AND DT 2008 AND VI 70 AND IP 4

Results: 55

Protein classification with imbalanced data.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1125, doi. 10.1002/prot.21870

By:

Zhao, Xing-Ming;
Li, Xin;
Chen, Luonan;
Aihara, Kazuyuki

Publication type:

Article

Crystal structure of the proline iminopeptidase-related protein TTHA1809 from Thermus thermophilus HB8.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1646, doi. 10.1002/prot.21892

By:

Okai, Masahiko;
Miyauchi, Yumiko;
Ebihara, Akio;
Lee, Woo Cheol;
Nagata, Koji;
Tanokura, Masaru

Publication type:

Article

Mn/Fe superoxide dismutase interaction fingerprints and prediction of oligomerization and metal cofactor from sequence.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1564, doi. 10.1002/prot.21650

By:

Wintjens, René;
Gilis, Dimitri;
Rooman, Marianne

Publication type:

Article

Characterization and structural modeling of a novel thermostable glycine oxidase from Geobacillus kaustophilus HTA426.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1429, doi. 10.1002/prot.21690

By:

Martínez-Martínez, Irene;
Navarro-Fernández, José;
García-Carmona, Francisco;
Takami, Hideto;
Sánchez-Ferrer, Álvaro

Publication type:

Article

Computational analysis of folding and mutation properties of C5 domain of myosin binding protein C.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1313, doi. 10.1002/prot.21621

By:

Guardiani, Carlo;
Cecconi, Fabio;
Livi, Roberto

Publication type:

Article

Molecular dynamics simulation study for LRH-1: Interaction with fragments of SHP and function of phospholipid ligand.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1527, doi. 10.1002/prot.21661

By:

Zhang, Tao;
Zhou, Jun-Hong;
Shi, Liang-Wei;
Zhu, Rui-Xin;
Chen, Min-Bo

Publication type:

Article

A diverse view of protein dynamics from NMR studies of HIV-1 protease flaps.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1408, doi. 10.1002/prot.21632

By:

Ishima, Rieko;
Louis, John M.

Publication type:

Article

Efficient comprehensive scoring of docked protein complexes using probabilistic support vector machines.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1367, doi. 10.1002/prot.21603

By:

Martin, Oliver;
Schomburg, Dietmar

Publication type:

Article

Operational definition of intrinsically unstructured protein sequences based on susceptibility to the 20S proteasome.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1357, doi. 10.1002/prot.21614

By:

Tsvetkov, Peter;
Asher, Gad;
Paz, Aviv;
Reuven, Nina;
Sussman, Joel L.;
Silman, Israel;
Shaul, Yosef

Publication type:

Article

A knowledge-based forcefield for protein-protein interface design.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1540, doi. 10.1002/prot.21694

By:

Clark, Louis A.;
van Vlijmen, Herman W. T.

Publication type:

Article

Dynamic property is a key determinant for protein-protein interactions.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1323, doi. 10.1002/prot.21625

By:

Bai, Hongjun;
Ma, Wenzhe;
Liu, Shiyong;
Lai, Luhua

Publication type:

Article

Mechanistic insights into the inhibition of prostate specific antigen by β-lactam class compounds.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1416, doi. 10.1002/prot.21676

By:

Singh, Pratap;
Williams, Simon A.;
Shah, Meha H.;
Lectka, Thomas;
Pritchard, Gareth J.;
Isaacs, John T.;
Denmeade, Samuel R.

Publication type:

Article

Receptor-specific scoring functions derived from quantum chemical models improve affinity estimates for in-silico drug discovery.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1264, doi. 10.1002/prot.21607

By:

Fischer, Bernhard;
Fukuzawa, Kaori;
Wenzel, Wolfgang

Publication type:

Article

Water penetration in the low and high pressure native states of ubiquitin.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1175, doi. 10.1002/prot.21562

By:

Day, Ryan;
García, Angel E.

Publication type:

Article

Evaluating conformational changes in protein structures binding RNA.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1518, doi. 10.1002/prot.21647

By:

Ellis, Jonathan J.;
Jones, Susan

Publication type:

Article

Do collagenases unwind triple-helical collagen before peptide bond hydrolysis? Reinterpreting experimental observations with mathematical models.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1154, doi. 10.1002/prot.21687

By:

Nerenberg, Paul S.;
Salsas-Escat, Ramon;
Stultz, Collin M.

Publication type:

Article

Full correlation analysis of conformational protein dynamics.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1294, doi. 10.1002/prot.21618

By:

Lange, Oliver F.;
Grubmüller, Helmut

Publication type:

Article

Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1332, doi. 10.1002/prot.21629

By:

Johansson, Anna C.V.;
Lindahl, Erik

Publication type:

Article

Protonless 13C direct detection NMR: Characterization of the 37 kDa trimeric protein CutA1.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1196, doi. 10.1002/prot.21577

By:

Bertini, Ivano;
Jiménez, Beatriz;
Pierattelli, Roberta;
Wedd, Anthony G.;
Xiao, Zhiguang

Publication type:

Article

NMR structure of protein Cgl2762 from Corynebacterium glutamicum implicated in DNA transposition reveals a helix-turn-helix motif attached to a flexibly disordered leucine zipper.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1650, doi. 10.1002/prot.21840

By:

Singarapu, Kiran Kumar;
Xiao, Rong;
Sukumaran, Dinesh K.;
Acton, Thomas;
Montelione, Gaetano T.;
Szyperski, Thomas

Publication type:

Article

HingeProt: Automated prediction of hinges in protein structures.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1219, doi. 10.1002/prot.21613

By:

Emekli, Ugur;
Schneidman-Duhovny, Dina;
Wolfson, Haim J.;
Nussinov, Ruth;
Haliloglu, Turkan

Publication type:

Article

Crystal structure of the PH1932 protein, a unique archaeal ArsR type winged-HTH transcription factor from Pyrococcus horikoshii OT3.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1631, doi. 10.1002/prot.21851

By:

Itou, Hiroshi;
Yao, Min;
Watanabe, Nobuhisa;
Tanaka, Isao

Publication type:

Article

Crystal structure of human cyclophilin D in complex with its inhibitor, cyclosporin A at 0.96-Å resolution.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1635, doi. 10.1002/prot.21855

By:

Kajitani, Kenji;
Fujihashi, Masahiro;
Kobayashi, Yukiko;
Shimizu, Shigeomi;
Tsujimoto, Yoshihide;
Miki, Kunio

Publication type:

Article

Crystal structure of human cellular retinol-binding protein II to 1.2 Å resolution.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1626, doi. 10.1002/prot.21848

By:

Tarter, Marina;
Capaldi, Stefano;
Carrizo, Maria E.;
Ambrosi, Emmanuele;
Perduca, Massimiliano;
Monaco, Hugo L.

Publication type:

Article

Evaluating protein:protein complex formation using synchrotron radiation circular dichroism spectroscopy.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1142, doi. 10.1002/prot.21631

By:

Cowieson, Nathan P.;
Miles, Andrew J.;
Robin, Gautier;
Forwood, Jade K.;
Kobe, Bostjan;
Martin, Jennifer L.;
Wallace, B. A.

Publication type:

Article

Biophysical characterization of Vpu from HIV-1 suggests a channel-pore dualism.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1488, doi. 10.1002/prot.21642

By:

Mehnert, T.;
Routh, A.;
Judge, P. J.;
Lam, Y. H.;
Fischer, D.;
Watts, A.;
Fischer, W. B.

Publication type:

Article

In silico study of the human rhodopsin and meta rhodopsin II/S-arrestin complexes: Impact of single point mutations related to retina degenerative diseases.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1133, doi. 10.1002/prot.21873

By:

Mokarzel-Falcón, Leonardo;
Padrón-García, Juan Alexander;
Carrasco-Velar, Ramón;
Berry, Colin;
Montero-Cabrera, Luis A.

Publication type:

Article

Prediction of protein structure from ideal forms.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1610, doi. 10.1002/prot.21913

By:

Taylor, William R.;
Bartlett, Gail J.;
Chelliah, Vijayalakshmi;
Klose, Daniel;
Lin, Kuang;
Sheldon, Tom;
Jonassen, Inge

Publication type:

Article

The HhH domain of the human DNA repair protein XPF forms stable homodimers.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1551, doi. 10.1002/prot.21635

By:

Das, Devashish;
Tripsianes, Konstantinos;
Jaspers, Nicolaas G. J.;
Hoeijmakers, Jan H. J.;
Kaptein, Robert;
Boelens, Rolf;
Folkers, Gert E.

Publication type:

Article

Assessing the reliability of sequence similarities detected through hydrophobic cluster analysis.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1588, doi. 10.1002/prot.21803

By:

Silva, Pedro J.

Publication type:

Article

Screening of the active site from water by the incoming ligand triggers catalysis and inhibition in serine proteases.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1578, doi. 10.1002/prot.21727

By:

Shokhen, Michael;
Khazanov, Netaly;
Albeck, Amnon

Publication type:

Article

Energetics of protein homodimerization: Effects of water sequestering on the formation of β-lactoglobulin dimer.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1475, doi. 10.1002/prot.21639

By:

Bello, Martiniano;
Pérez-Hernández, Gerardo;
Fernández-Velasco, D. Alejandro;
Arreguín-Espinosa, Roberto;
García-Hernández, Enrique

Publication type:

Article

Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single-point mutation of a β-sheet miniprotein.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1185, doi. 10.1002/prot.21565

By:

Muff, Stefanie;
Caflisch, Amedeo

Publication type:

Article

Dynamics of group II chaperonin and prefoldin probed by 13C NMR spectroscopy.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1257, doi. 10.1002/prot.21606

By:

Kurimoto, Eiji;
Nishi, Yohei;
Yamaguchi, Yoshiki;
Zako, Tamotsu;
Iizuka, Ryo;
Ide, Naoki;
Yohda, Masafumi;
Kato, Koichi

Publication type:

Article

Thermostable variants of the recombinant xylanase a from Bacillus subtilis produced by directed evolution show reduced heat capacity changes.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1280, doi. 10.1002/prot.21617

By:

Ruller, Roberto;
Deliberto, Laila;
Ferreira, Tatiana Lopes;
Ward, Richard J.

Publication type:

Article

Structural basis of octanoic acid recognition by lipoate-protein ligase B.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1620, doi. 10.1002/prot.21843

By:

Kim, Do Jin;
Lee, Sang Jae;
Kim, Hyoun Sook;
Kim, Kyoung Hoon;
Lee, Hyung Ho;
Yoon, Hye Jin;
Suh, Se Won

Publication type:

Article

Differential native state ruggedness of the two Ca2+-binding domains in a Ca2+ sensor protein.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1147, doi. 10.1002/prot.21751

By:

Krishna Mohan, P. M.;
Mukherjee, Sulakshana;
Chary, Kandala V. R.

Publication type:

Article

Prolylproline unit in model peptides and in fragments from databases.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1389, doi. 10.1002/prot.21630

By:

Hudáky, Ilona;
Perczel, András

Publication type:

Article

Exploiting 3D structural templates for detection of metal-binding sites in protein structures.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1206, doi. 10.1002/prot.21601

By:

Goyal, Kshama;
Mande, Shekhar C.

Publication type:

Article

A finite element framework for computation of protein normal modes and mechanical response.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1595, doi. 10.1002/prot.21708

By:

Bathe, Mark

Publication type:

Article

Sampling of near-native protein conformations during protein structure refinement using a coarse-grained model, normal modes, and molecular dynamics simulations.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1345, doi. 10.1002/prot.21674

By:

Stumpff-Kane, Andrew W.;
Maksimiak, Katarzyna;
Lee, Michael S.;
Feig, Michael

Publication type:

Article

Predicting experimental properties of integral membrane proteins by a naive Bayes approach.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1243, doi. 10.1002/prot.21605

By:

Martin-Galiano, Antonio J.;
Smialowski, Pawel;
Frishman, Dmitrij

Publication type:

Article

Automated prediction of ligand-binding sites in proteins.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1506, doi. 10.1002/prot.21645

By:

Harris, Rodney;
Olson, Arthur J.;
Goodsell, David S.

Publication type:

Article

Discrimination of mesophilic and thermophilic proteins using machine learning algorithms.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1274, doi. 10.1002/prot.21616

By:

Gromiha, M. Michael;
Suresh, M. Xavier

Publication type:

Article

Ion exclusion mechanism in aquaporin at an atomistic level.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1442, doi. 10.1002/prot.21696

By:

Ko, Youn Jo;
Huh, June;
Jo, Won Ho

Publication type:

Article

Assembly of the oncogenic DNA-binding complex LMO2-Ldb1-TAL1-E12.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1461, doi. 10.1002/prot.21638

By:

Ryan, Daniel P.;
Duncan, Jaimee L.;
Lee, Christopher;
Kuchel, Philip W.;
Matthews, Jacqueline M.

Publication type:

Article

Structure of aspartate racemase complexed with a dual substrate analogue, citric acid, and implications for the reaction mechanism.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1167, doi. 10.1002/prot.21528

By:

Ohtaki, Akashi;
Nakano, Yohsuke;
Iizuka, Ryo;
Arakawa, Takatoshi;
Yamada, Kazuhiro;
Odaka, Masafumi;
Yohda, Masafumi

Publication type:

Article

A unique catalytic triad revealed by the crystal structure of APE0912, a short-chain dehydrogenase/reductase family protein from Aeropyrum pernix K1.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1640, doi. 10.1002/prot.21860

By:

Yamamura, Akihiro;
Ichimura, Takefumi;
Mimoto, Futa;
Ohtsuka, Jun;
Miyazono, Ken-Ichi;
Okai, Masahiko;
Kamo, Masayuki;
Lee, Woo-Cheol;
Nagata, Koji;
Tanokura, Masaru

Publication type:

Article

Correction to the article 'Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations'.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1655, doi. 10.1002/prot.21916

By:

Johansson, Anna C. V.;
Lindahl, Erik

Publication type:

Article

MALIDUP: A database of manually constructed structure alignments for duplicated domain pairs.

Published in:

Proteins, 2008, v. 70, n. 4, p. 1162, doi. 10.1002/prot.21783

By:

Cheng, Hua;
Kim, Bong-Hyun;
Grishin, Nick V.

Publication type:

Article