Works matching IS 08873585 AND DT 2008 AND VI 71 AND IP 4

Results: 44

Comparison of the efficiency of evolutionary change-based and side chain orientation-based fold recognition potentials.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1863, doi. 10.1002/prot.21871

By:

Vishnepolsky, Boris;
Managadze, Grigol;
Pirtskhalava, Malak

Publication type:

Article

Stacking efficiency and flexibility analysis of aromatic amino acids in cap-binding proteins.

Published in:

Proteins, 2008, v. 71, n. 4, p. 2026, doi. 10.1002/prot.21882

By:

Worch, Remigiusz;
Stolarski, Ryszard

Publication type:

Article

Computational prediction of the binding site of proteinase 3 to the plasma membrane.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1655, doi. 10.1002/prot.21853

By:

Hajjar, Eric;
Mihajlovic, Maja;
Witko-Sarsat, Véronique;
Lazaridis, Themis;
Reuter, Nathalie

Publication type:

Article

Response to András Szilágyi's Commentary.

Published in:

Proteins, 2008, v. 71, n. 4, p. 2089, doi. 10.1002/prot.22031

By:

Zbilut, Joseph P.;
Giuliani, Alessandro;
Webber, Charles L.

Publication type:

Article

pH sensitivity of type III secretion system tip proteins.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1830, doi. 10.1002/prot.21864

By:

Markham, Aaron P.;
Birket, Susan E.;
Picking, William D.;
Picking, Wendy L.;
Middaugh, C. Russell

Publication type:

Article

Conformational and dynamics changes induced by bile acids binding to chicken liver bile acid binding protein.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1889, doi. 10.1002/prot.21875

By:

Eberini, Ivano;
Guerini Rocco, Alessandro;
Ientile, Anna Rita;
Baptista, António M.;
Gianazza, Elisabetta;
Tomaselli, Simona;
Molinari, Henriette;
Ragona, Laura

Publication type:

Article

The solution structure of the outer membrane lipoprotein OmlA from Xanthomonas axonopodis pv. citri reveals a protein fold implicated in protein-protein interaction.

Published in:

Proteins, 2008, v. 71, n. 4, p. 2051, doi. 10.1002/prot.21886

By:

Vanini, Marina Marques Teixeira;
Spisni, Alberto;
Sforça, Maurício Luis;
Pertinhez, Thelma Aguiar;
Benedetti, Celso Eduardo

Publication type:

Article

The protein fluorescence and structural toolkit: Database and programs for the analysis of protein fluorescence and structural data.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1744, doi. 10.1002/prot.21857

By:

Shen, Chi;
Menon, Rajiv;
Das, Dipanwita;
Bansal, Nidhi;
Nahar, Neha;
Guduru, Neelima;
Jaegle, Stephen;
Peckham, Joan;
Reshetnyak, Yana K.

Publication type:

Article

Understanding of known drug-target interactions in the catalytic pocket of neuraminidase subtype N1.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1908, doi. 10.1002/prot.21897

By:

Malaisree, Maturos;
Rungrotmongkol, Thanyada;
Decha, Panita;
Intharathep, Pathumwadee;
Aruksakunwong, Ornjira;
Hannongbua, Supot

Publication type:

Article

Calcineurin B-like domains in the large regulatory α/β subunits of phosphorylase kinase.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1597, doi. 10.1002/prot.22006

By:

Carrière, Cathelène;
Mornon, Jean-Paul;
Venien-Bryan, Catherine;
Boisset, Nicolas;
Callebaut, Isabelle

Publication type:

Article

A combined approach of mass spectrometry, molecular modeling, and site-directed mutagenesis highlights key structural features responsible for the thermostability of Sulfolobus solfataricus carboxypeptidase.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1843, doi. 10.1002/prot.21868

By:

Sommaruga, Silvia;
De Palma, Antonella;
Mauri, Pier Luigi;
Trisciani, Manuela;
Basilico, Fabrizio;
Martelli, Pier Luigi;
Casadio, Rita;
Tortora, Paolo;
Occhipinti, Emanuela

Publication type:

Article

Complex assembly mechanism and an RNA-binding mode of the human p14-SF3b155 spliceosomal protein complex identified by NMR solution structure and functional analyses.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1617, doi. 10.1002/prot.21839

By:

Kuwasako, Kanako;
Dohmae, Naoshi;
Inoue, Mio;
Shirouzu, Mikako;
Taguchi, Seiichi;
Güntert, Peter;
Séraphin, Bertrand;
Muto, Yutaka;
Yokoyama, Shigeyuki

Publication type:

Article

Hydrophobic clusters in protein structures.

Published in:

Proteins, 2008, v. 71, n. 4, p. 2012, doi. 10.1002/prot.21881

By:

Arunachalam, J.;
Gautham, N.

Publication type:

Article

Exploring the protein G helix free-energy surface by solute tempering metadynamics.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1647, doi. 10.1002/prot.21852

By:

Camilloni, Carlo;
Provasi, Davide;
Tiana, Guido;
Broglia, Ricardo A.

Publication type:

Article

Overexpression, physicochemical characterization, and modeling of a hyperthermophilic pyrococcus furiosus type 2 IPP isomerase.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1699, doi. 10.1002/prot.21863

By:

Dutoit, Raphaël;
de Ruyck, Jérôme;
Durisotti, Virginie;
Legrain, Christianne;
Jacobs, Eric;
Wouters, Johan

Publication type:

Article

Water-mediated interactions between DNA and PhoB DNA-binding/transactivation domain: NMR-restrained molecular dynamics in explicit water environment.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1970, doi. 10.1002/prot.21874

By:

Yamane, Tsutomu;
Okamura, Hideyasu;
Ikeguchi, Mitsunori;
Nishimura, Yoshifumi;
Kidera, Akinori

Publication type:

Article

Using quantum mechanics to improve estimates of amino acid side chain rotamer energies.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1637, doi. 10.1002/prot.21845

By:

Renfrew, P. Douglas;
Butterfoss, Glenn L.;
Kuhlman, Brian

Publication type:

Article

Crystal structure of YagE, a putative DHDPS-like protein from Escherichia coli K12.

Published in:

Proteins, 2008, v. 71, n. 4, p. 2102, doi. 10.1002/prot.22023

By:

Manicka, Sankar;
Peleg, Yoav;
Unger, Tamar;
Albeck, Shira;
Dym, Orly;
Greenblatt, Harry M.;
Bourenkov, Gleb;
Lamzin, Victor;
Krishnaswamy, Sankaran;
Sussman, Joel L.

Publication type:

Article

Huntingtin interacting protein HYPK is intrinsically unstructured.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1686, doi. 10.1002/prot.21856

By:

Raychaudhuri, Swasti;
Majumder, Pritha;
Sarkar, Somosree;
Giri, Kalyan;
Mukhopadhyay, Debashis;
Bhattacharyya, Nitai P.

Publication type:

Article

Protein-protein docking by simulating the process of association subject to biochemical constraints.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1955, doi. 10.1002/prot.21867

By:

Motiejunas, Domantas;
Gabdoulline, Razif;
Wang, Ting;
Feldman-Salit, Anna;
Johann, Tim;
Winn, Peter J.;
Wade, Rebecca C.

Publication type:

Article

Statistical geometry based prediction of nonsynonymous SNP functional effects using random forest and neuro-fuzzy classifiers.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1930, doi. 10.1002/prot.21838

By:

Barenboim, Maxim;
Masso, Majid;
Vaisman, Iosif I.;
Jamison, D. Curtis

Publication type:

Article

Refinement of noncalorimetric determination of the change in heat capacity, Δ Cp, of protein unfolding and validation across a wide temperature range.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1607, doi. 10.1002/prot.22016

By:

Talla-Singh, Deepika;
Stites, Wesley E.

Publication type:

Article

Insights into activation and RNA binding of trp RNA-binding attenuation protein (TRAP) through all-atom simulations.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1995, doi. 10.1002/prot.21878

By:

Murtola, Teemu;
Vattulainen, Ilpo;
Falck, Emma

Publication type:

Article

Identifying folding nucleus based on residue contact networks of proteins.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1899, doi. 10.1002/prot.21891

By:

Li, Jie;
Wang, Jun;
Wang, Wei

Publication type:

Article

A mathematically related singularity and the maximum size of protein domains.

Published in:

Proteins, 2008, v. 71, n. 4, p. 2086, doi. 10.1002/prot.22000

By:

Szilágyi, András

Publication type:

Article

The conformational plasticity of calmodulin upon calcium complexation gives a model of its interaction with the oedema factor of Bacillus anthracis.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1813, doi. 10.1002/prot.21862

By:

Laine, Elodie;
Yoneda, Julliane D.;
Blondel, Arnaud;
Malliavin, Thérèse E.

Publication type:

Article

Crystal structure of single-domain VL of an anti-DNA binding antibody 3D8 scFv and its active site revealed by complex structures of a small molecule and metals.

Published in:

Proteins, 2008, v. 71, n. 4, p. 2091, doi. 10.1002/prot.22011

By:

Park, Suk-Youl;
Lee, Woo-Ram;
Lee, Suk-Chan;
Kwon, Myung-Hee;
Kim, Yong-Sung;
Kim, Jeong-Sun

Publication type:

Article

Sequence-structure-function analysis of the bifunctional enzyme MnmC that catalyses the last two steps in the biosynthesis of hypermodified nucleoside mnm5s2U in tRNA.

Published in:

Proteins, 2008, v. 71, n. 4, p. 2076, doi. 10.1002/prot.21918

By:

Roovers, Martine;
Oudjama, Yamina;
Kaminska, Katarzyna H.;
Purta, Elzbieta;
Caillet, Joël;
Droogmans, Louis;
Bujnicki, Janusz M.

Publication type:

Article

Analyzing and modeling the inhibitory effect of phosphatidic acid on the GTP-γ-S binding activity of Goα.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1732, doi. 10.1002/prot.21826

By:

Qu, Liang;
Wan, Jia;
Cao, Yu;
Zhang, Yinghao;
Chen, Runsheng;
Huang, Youguo

Publication type:

Article

Tandem use of X-ray crystallography and mass spectrometry to obtain ab initio the complete and exact amino acids sequence of HPBP, a human 38-kDa apolipoprotein.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1708, doi. 10.1002/prot.21866

By:

Diemer, Hélène;
Elias, Mikael;
Renault, Frédérique;
Rochu, Daniel;
Contreras-Martel, Carlos;
Schaeffer, Christine;
Van Dorsselaer, Alain;
Chabriere, Eric

Publication type:

Article

Functional and structural features of the oxyanion hole in a thermophilic esterase from Alicyclobacillus acidocaldarius.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1721, doi. 10.1002/prot.21877

By:

Mandrich, Luigi;
Menchise, Valeria;
Alterio, Vincenzo;
De Simone, Giuseppina;
Pedone, Carlo;
Rossi, Mosè;
Manco, Giuseppe

Publication type:

Article

Functional and computational studies of the ligand-associated metal binding site of β3 integrins.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1779, doi. 10.1002/prot.21859

By:

Murcia, Marta;
Jirouskova, Marketa;
Li, Jihong;
Coller, Barry S.;
Filizola, Marta

Publication type:

Article

Interdomain cooperativity of calmodulin bound to melittin preferentially increases calcium affinity of sites I and II.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1792, doi. 10.1002/prot.21861

By:

Newman, Rhonda A.;
Van Scyoc, Wendy S.;
Sorensen, Brenda R.;
Jaren, Olav R.;
Shea, Madeline A.

Publication type:

Article

Expanding GPCR homology model binding sites via a balloon potential: A molecular dynamics refinement approach.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1919, doi. 10.1002/prot.21906

By:

Kimura, S. Roy;
Tebben, Andrew J.;
Langley, David R.

Publication type:

Article

Toxoplasma gondii ferredoxin-NADP+ reductase: Role of ionic interactions in stabilization of native conformation and structural cooperativity.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1879, doi. 10.1002/prot.21872

By:

Singh, Kulwant;
Bhakuni, Vinod

Publication type:

Article

A phospho-sugar binding domain homologous to NagB enzymes regulates the activity of the central glycolytic genes repressor.

Published in:

Proteins, 2008, v. 71, n. 4, p. 2038, doi. 10.1002/prot.21883

By:

Doan, Thierry;
Martin, Laetitia;
Zorrilla, Silvia;
Chaix, Denis;
Aymerich, Stéphane;
Labesse, Gilles;
Declerck, Nathalie

Publication type:

Article

Solvent-exposed residues located in the β-sheet modulate the stability of the tetramerization domain of p53-A structural and combinatorial approach.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1670, doi. 10.1002/prot.21854

By:

Mora, Puig;
Carbajo, Rodrigo J.;
Pineda-Lucena, Antonio;
Sánchez del Pino, Manuel M.;
Pérez-Payá, Enrique

Publication type:

Article

An insight into the general relationship between the three dimensional structures of enzymes and their electronic wave functions: Implication for the prediction of functional sites of enzymes.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1940, doi. 10.1002/prot.21865

By:

Fukushima, K.;
Wada, M.;
Sakurai, M.

Publication type:

Article

The type IA topoisomerase catalytic cycle: A normal mode analysis and molecular dynamics simulation.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1984, doi. 10.1002/prot.21876

By:

Xiong, Bing;
Burk, David L.;
Shen, Jianhua;
Luo, Xiaomin;
Liu, Hong;
Shen, Jingkang;
Berghuis, Albert M.

Publication type:

Article

Crystal structure of a novel non-Pfam protein AF1514 from Archeoglobus fulgidus DSM 4304 solved by S-SAD using a Cr X-ray source.

Published in:

Proteins, 2008, v. 71, n. 4, p. 2109, doi. 10.1002/prot.22025

By:

Li, Yang;
Bahti, Pazilat;
Shaw, Neil;
Song, Gaojie;
Chen, Shunmei;
Zhang, Xuejun;
Zhang, Min;
Cheng, Chongyun;
Yin, Jie;
Zhu, Jin-Yi;
Zhang, Hua;
Che, Dongsheng;
Xu, Hao;
Abbas, Abdulla;
Wang, Bi-Cheng;
Liu, Zhi-Jie

Publication type:

Article

A simple and fuzzy method to align and compare druggable ligand-binding sites.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1755, doi. 10.1002/prot.21858

By:

Schalon, Claire;
Surgand, Jean-Sébastien;
Kellenberger, Esther;
Rognan, Didier

Publication type:

Article

The X-ray structure of N-methyltryptophan oxidase reveals the structural determinants of substrate specificity.

Published in:

Proteins, 2008, v. 71, n. 4, p. 2065, doi. 10.1002/prot.21898

By:

Ilari, Andrea;
Bonamore, Alessandra;
Franceschini, Stefano;
Fiorillo, Annarita;
Boffi, Alberto;
Colotti, Gianni

Publication type:

Article

Structure-function relationship of inhibitory Smads: Structural flexibility contributes to functional divergence.

Published in:

Proteins, 2008, v. 71, n. 4, p. 1853, doi. 10.1002/prot.21869

By:

Hariharan, Ramkumar;
Pillai, M. Radhakrishna

Publication type:

Article

Crystal structure of uncharacterized protein TTHA1756 from Thermus thermophilus HB8: Structural variety in UPF0150 family proteins.

Published in:

Proteins, 2008, v. 71, n. 4, p. 2097, doi. 10.1002/prot.22018

By:

Ebihara, Akio;
Manzoku, Miho;
Iino, Hitoshi;
Kanagawa, Mayumi;
Shinkai, Akeo;
Yokoyama, Shigeyuki;
Kuramitsu, Seiki

Publication type:

Article