Works matching IS 08873585 AND DT 2006 AND VI 63 AND IP 4

Results: 45

A simple clustering algorithm can be accurate enough for use in calculations of p Ks in macromolecules.

Published in:

Proteins, 2006, v. 63, n. 4, p. 928, doi. 10.1002/prot.20922

By:

Myers, Jonathan;
Grothaus, Greg;
Narayanan, Shivaram;
Onufriev, Alexey

Publication type:

Article

Solution structure of the plant defensin VrD1 from mung bean and its possible role in insecticidal activity against bruchids.

Published in:

Proteins, 2006, v. 63, n. 4, p. 777, doi. 10.1002/prot.20962

By:

Liu, Yaw-Jen;
Cheng, Chao-Sheng;
Lai, Szu-Ming;
Hsu, Ming-Pin;
Chen, Ching-San;
Lyu, Ping-Chiang

Publication type:

Article

Correlated mutations: Advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families.

Published in:

Proteins, 2006, v. 63, n. 4, p. 832, doi. 10.1002/prot.20933

By:

Halperin, Inbal;
Wolfson, Haim;
Nussinov, Ruth

Publication type:

Article

Detailed microscopic study of the full zipA:FtsZ interface.

Published in:

Proteins, 2006, v. 63, n. 4, p. 811, doi. 10.1002/prot.20944

By:

Moreira, I.S.;
Fernandes, P.A.;
Ramos, M.J.

Publication type:

Article

Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets.

Published in:

Proteins, 2006, v. 63, n. 4, p. 986, doi. 10.1002/prot.20881

By:

Melo, Francisco;
Marti-Renom, Marc A.

Publication type:

Article

Substructural cooperativity and parallel versus sequential events during protein unfolding.

Published in:

Proteins, 2006, v. 63, n. 4, p. 1052, doi. 10.1002/prot.20966

By:

Reich, Lothar;
Weikl, Thomas R.

Publication type:

Article

Crystal structures of two putative phosphoheptose isomerases.

Published in:

Proteins, 2006, v. 63, n. 4, p. 1092, doi. 10.1002/prot.20908

By:

Seetharaman, Jayaraman;
Rajashankar, Kanagalaghatta R.;
Solorzano, Veronica;
Kniewel, Ryan;
Lima, Christopher D.;
Bonanno, Jeffrey B.;
Burley, Stephen K.;
Swaminathan, Subramanyam

Publication type:

Article

Codep: Maximizing co-evolutionary interdependencies to discover interacting proteins.

Published in:

Proteins, 2006, v. 63, n. 4, p. 822, doi. 10.1002/prot.20948

By:

Tillier, Elisabeth R. M.;
Biro, Laurence;
Li, Ginny;
Tillo, Desiree

Publication type:

Article

Crystal structure of VC0702 at 2.0 Å: Conserved hypothetical protein from Vibrio cholerae.

Published in:

Proteins, 2006, v. 63, n. 4, p. 733, doi. 10.1002/prot.20919

By:

Ni, Shuisong;
Forouhar, Farhad;
Bussiere, Dirksen E.;
Robinson, Howard;
Kennedy, Michael A.

Publication type:

Article

Structural characterization of an iron-sulfur cluster assembly protein IscU in a zinc-bound form.

Published in:

Proteins, 2006, v. 63, n. 4, p. 1137, doi. 10.1002/prot.20856

By:

Liu, Jinyu;
Oganesyan, Natalia;
Shin, Dong-Hae;
Jancarik, Jarmila;
Yokota, Hisao;
Kim, Rosalind;
Kim, Sung-Hou

Publication type:

Article

Chemical compound navigator: A web-based chem-BLAST, chemical taxonomy-based search engine for browsing compounds.

Published in:

Proteins, 2006, v. 63, n. 4, p. 907, doi. 10.1002/prot.20914

By:

Prasanna, M.D.;
Vondrasek, Jiri;
Wlodawer, Alexander;
Rodriguez, H.;
Bhat, T. N.

Publication type:

Article

Empirical potential function for simplified protein models: Combining contact and local sequence-structure descriptors.

Published in:

Proteins, 2006, v. 63, n. 4, p. 949, doi. 10.1002/prot.20809

By:

Zhang, Jinfeng;
Chen, Rong;
Liang, Jie

Publication type:

Article

Scoring a diverse set of high-quality docked conformations: A metascore based on electrostatic and desolvation interactions.

Published in:

Proteins, 2006, v. 63, n. 4, p. 868, doi. 10.1002/prot.20932

By:

Camacho, Carlos J.;
Ma, Hui;
Champ, P. Christoph

Publication type:

Article

Functional grouping based on signatures in protein termini.

Published in:

Proteins, 2006, v. 63, n. 4, p. 996, doi. 10.1002/prot.20903

By:

Bahir, Iris;
Linial, Michal

Publication type:

Article

Reducing CDK4/6-p16<sup>INK4a</sup> interface. Computational alanine scanning of a peptide bound to CDK6 protein.

Published in:

Proteins, 2006, v. 63, n. 4, p. 797, doi. 10.1002/prot.20943

By:

Villacañas, Óscar;
Rubio-Martinez, Jaime

Publication type:

Article

Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 Å resolution.

Published in:

Proteins, 2006, v. 63, n. 4, p. 1106, doi. 10.1002/prot.20650

By:

Mathews, Irimpan I.;
Krishna, S. Sri;
Schwarzenbacher, Robert;
McMullan, Daniel;
Abdubek, Polat;
Ambing, Eileen;
Canaves, Jaume M.;
Chiu, Hsiu-Ju;
Deacon, Ashley M.;
DiDonato, Michael;
Elsliger, Marc-André;
Godzik, Adam;
Grittini, Carina;
Grzechnik, Slawomir K.;
Hale, Joanna;
Hampton, Eric;
Han, Gye Won;
Haugen, Justin;
Jaroszewski, Lukasz;
Klock, Heath E.

Publication type:

Article

Structures of intact glycoproteins from vibrational circular dichroism.

Published in:

Proteins, 2006, v. 63, n. 4, p. 768, doi. 10.1002/prot.20884

By:

Shanmugam, Ganesh;
Polavarapu, Prasad L.

Publication type:

Article

Novel, structure-based mechanism for uridylylation of the genome-linked peptide (VPg) of picornaviruses.

Published in:

Proteins, 2006, v. 63, n. 4, p. 719, doi. 10.1002/prot.20891

By:

Schein, Catherine H.;
Volk, David E.;
Oezguen, Numan;
Paul, Aniko

Publication type:

Article

Multiscale modeling of macromolecular conformational changes combining concepts from rigidity and elastic network theory.

Published in:

Proteins, 2006, v. 63, n. 4, p. 1038, doi. 10.1002/prot.20907

By:

Ahmed, Aqeel;
Gohlke, Holger

Publication type:

Article

Conformational flexibility may explain multiple cellular roles of PEST motifs.

Published in:

Proteins, 2006, v. 63, n. 4, p. 727, doi. 10.1002/prot.20918

By:

Sandhu, Kuljeet Singh;
Dash, Debasis

Publication type:

Article

Crystal structure of human protein tyrosine phosphatase 14 (PTPN14) at 1.65-Å resolution.

Published in:

Proteins, 2006, v. 63, n. 4, p. 1132, doi. 10.1002/prot.20958

By:

Barr, Alastair J.;
Debreczeni, Judit É.;
Eswaran, Jeyanthy;
Knapp, Stefan

Publication type:

Article

Crystal structure of human spermidine/spermine N<sup>1</sup>-acetyltransferase (hSSAT): The first structure of a new sequence family of transferase homologous superfamily.

Published in:

Proteins, 2006, v. 63, n. 4, p. 1127, doi. 10.1002/prot.20965

By:

Zhu, Yong-Qun;
Zhu, De-Yu;
Yin, Lei;
Zhang, Ying;
Vonrhein, Clemens;
Wang, Da-Cheng

Publication type:

Article

Discrimination of outer membrane proteins using machine learning algorithms.

Published in:

Proteins, 2006, v. 63, n. 4, p. 1031, doi. 10.1002/prot.20929

By:

Gromiha, M. Michael;
Suwa, Makiko

Publication type:

Article

A two-entropies analysis to identify functional positions in the transmembrane region of class A G protein-coupled receptors.

Published in:

Proteins, 2006, v. 63, n. 4, p. 1018, doi. 10.1002/prot.20899

By:

Ye, Kai;
Lameijer, Eric-Wubbo M.;
Beukers, Margot W.;
IJzerman, Adriaan P.

Publication type:

Article

Theoretical model of restriction endonuclease HpaI in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis.

Published in:

Proteins, 2006, v. 63, n. 4, p. 1059, doi. 10.1002/prot.20920

By:

Skowronek, Krzysztof J.;
Kosinski, Jan;
Bujnicki, Janusz M.

Publication type:

Article

Effective handling of induced-fit motion in flexible docking.

Published in:

Proteins, 2006, v. 63, n. 4, p. 878, doi. 10.1002/prot.20931

By:

Mizutani, Miho Yamada;
Takamatsu, Yoshihiro;
Ichinose, Tazuko;
Nakamura, Kensuke;
Itai, Akiko

Publication type:

Article

Fold recognition and accurate sequence-structure alignment of sequences directing β-sheet proteins.

Published in:

Proteins, 2006, v. 63, n. 4, p. 976, doi. 10.1002/prot.20942

By:

McDonnell, Andrew V.;
Menke, Matthew;
Palmer, Nathan;
King, Jonathan;
Cowen, Lenore;
Berger, Bonnie

Publication type:

Article

Structural analysis of the transcriptional regulator homolog protein from Pyrococcus horikoshii OT3.

Published in:

Proteins, 2006, v. 63, n. 4, p. 1084, doi. 10.1002/prot.20913

By:

Okada, Ui;
Sakai, Naoki;
Yao, Min;
Watanabe, Nobuhisa;
Tanaka, Isao

Publication type:

Article

Crystal structure of a putative HTH-type transcriptional regulator yxaF from Bacillus subtilis.

Published in:

Proteins, 2006, v. 63, n. 4, p. 1087, doi. 10.1002/prot.20924

By:

Seetharaman, Jayaraman;
Kumaran, Desigan;
Bonanno, Jeffrey B.;
Burley, Stephen K.;
Swaminathan, Subramanyam

Publication type:

Article

Effect of pH on the structure and stability of Bacillus circulans ssp. alkalophilus phosphoserine aminotransferase: Thermodynamic and crystallographic studies.

Published in:

Proteins, 2006, v. 63, n. 4, p. 742, doi. 10.1002/prot.20935

By:

Kapetaniou, Evangelia G.;
Thanassoulas, Angelos;
Dubnovitsky, Anatoly P.;
Nounesis, George;
Papageorgiou, Anastassios C.

Publication type:

Article

Nearest-neighbor effects and structural preferences in dipeptides are a function of the electronic properties of amino acid side-chains.

Published in:

Proteins, 2006, v. 63, n. 4, p. 939, doi. 10.1002/prot.20906

By:

Dwyer, Donard S.

Publication type:

Article

Modeling and functional analysis of AEBP1, a transcriptional repressor.

Published in:

Proteins, 2006, v. 63, n. 4, p. 1069, doi. 10.1002/prot.20946

By:

Lyons, Peter J.;
Mattatall, Neil R.;
Ro, Hyo-Sung

Publication type:

Article

Interdomain mobility in di-ubiquitin revealed by NMR.

Published in:

Proteins, 2006, v. 63, n. 4, p. 787, doi. 10.1002/prot.20917

By:

Ryabov, Yaroslav;
Fushman, David

Publication type:

Article

Crystal structure of TM1367 from Thermotoga maritima at 1.90 Å resolution reveals an atypical member of the cyclophilin (peptidylprolyl isomerase) fold.

Published in:

Proteins, 2006, v. 63, n. 4, p. 1112, doi. 10.1002/prot.20894

By:

Jin, Kevin Kai;
Krishna, S. Sri;
Schwarzenbacher, Robert;
McMullan, Daniel;
Abdubek, Polat;
Agarwalla, Sanjay;
Ambing, Eileen;
Axelrod, Herbert;
Canaves, Jaume M.;
Chiu, Hsiu-Ju;
Deacon, Ashley M.;
DiDonato, Michael;
Elsliger, Marc-André;
Feuerhelm, Julie;
Godzik, Adam;
Grittini, Carina;
Grzechnik, Slawomir K.;
Hale, Joanna;
Hampton, Eric;
Haugen, Justin

Publication type:

Article

The crystal structure of human muscle glycogen phosphorylase a with bound glucose and AMP: An intermediate conformation with T-state and R-state features.

Published in:

Proteins, 2006, v. 63, n. 4, p. 1123, doi. 10.1002/prot.20939

By:

Lukacs, Christine M.;
Oikonomakos, Nikos G.;
Crowther, Robert L.;
Hong, Li-Na;
Kammlott, R. Ursula;
Levin, Wayne;
Li, Shirley;
Liu, Chao-Min;
Lucas-McGady, Debra;
Pietranico, Sherrie;
Reik, Linda

Publication type:

Article

Reconciling the 'old' and 'new' views of protein allostery: A molecular simulation study of chemotaxis Y protein (CheY).

Published in:

Proteins, 2006, v. 63, n. 4, p. 846, doi. 10.1002/prot.20893

By:

Formaneck, Mark S.;
Ma, Liang;
Cui, Qiang

Publication type:

Article

Crystal structure of an RtcB homolog protein (PH1602-extein protein) from Pyrococcus horikoshii reveals a novel fold.

Published in:

Proteins, 2006, v. 63, n. 4, p. 1119, doi. 10.1002/prot.20912

By:

Okada, Chiaki;
Maegawa, Yuki;
Yao, Min;
Tanaka, Isao

Publication type:

Article

D-Trehalose/ D-maltose-binding protein from the hyperthermophilic archaeon Thermococcus litoralis: The binding of trehalose and maltose results in different protein conformational states.

Published in:

Proteins, 2006, v. 63, n. 4, p. 754, doi. 10.1002/prot.20952

By:

Herman, Petr;
Staiano, Maria;
Marabotti, Anna;
Varriale, Antonio;
Scirè, Andrea;
Tanfani, Fabio;
Vecer, Jaroslav;
Rossi, Mose';
D'Auria, Sabato

Publication type:

Article

QBES: Predicting real values of solvent accessibility from sequences by efficient, constrained energy optimization.

Published in:

Proteins, 2006, v. 63, n. 4, p. 961, doi. 10.1002/prot.20934

By:

Xu, Zhigang;
Zhang, Chi;
Liu, Song;
Zhou, Yaoqi

Publication type:

Article

Terminal ion pairs stabilize the second β-hairpin of the B1 domain of protein G.

Published in:

Proteins, 2006, v. 63, n. 4, p. 1005, doi. 10.1002/prot.20916

By:

Huyghues-Despointes, Beatrice M. P.;
Qu, Xiaotoa;
Tsai, Jerry;
Scholtz, J. Martin

Publication type:

Article

Polyglutamine repeats and β-helix structure: Molecular dynamics study.

Published in:

Proteins, 2006, v. 63, n. 4, p. 918, doi. 10.1002/prot.20941

By:

Merlino, Antonello;
Esposito, Luciana;
Vitagliano, Luigi

Publication type:

Article

ARTIST: An activated method in internal coordinate space for sampling protein energy landscapes.

Published in:

Proteins, 2006, v. 63, n. 4, p. 967, doi. 10.1002/prot.20938

By:

Yun, Mi-Ran;
Lavery, R.;
Mousseau, N.;
Zakrzewska, K.;
Derreumaux, P.

Publication type:

Article

On the nature of cavities on protein surfaces: Application to the identification of drug-binding sites.

Published in:

Proteins, 2006, v. 63, n. 4, p. 892, doi. 10.1002/prot.20897

By:

Nayal, Murad;
Honig, Barry

Publication type:

Article

1.6 Å Crystal structure of a PA2721 protein from pseudomonas aeruginosa-A potential drug-resistance protein.

Published in:

Proteins, 2006, v. 63, n. 4, p. 1102, doi. 10.1002/prot.20659

By:

Nocek, B.;
Cuff, M.;
Evdokimova, E.;
Edwards, A.;
Joachimiak, A.;
Savchenko, A.

Publication type:

Article

Crystal structure of hypothetical protein YfiH from Shigella flexneri at 2 Å resolution.

Published in:

Proteins, 2006, v. 63, n. 4, p. 1097, doi. 10.1002/prot.20589

By:

Kim, Youngchang;
Maltseva, Natalia;
Dementieva, Irina;
Collart, Frank;
Holzle, Denise;
Joachimiak, Andrzej

Publication type:

Article