Volume 60; Issue 2

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Proteins: Structure, Function, and Bioinformatics
Volume 60; Issue 2

Proteins: Structure, Function, and Bioinformatics

Volume 60; Issue 2

1

Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures

Raúl Méndez, Raphaël Leplae, Marc F. Lensink, Shoshana J. Wodak

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 460 KB

english, 2005

2

Sailing the route from Gaeta, Italy, to CAPRI

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 27 KB

english, 2005

3

The targets of CAPRI rounds 3–5

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 223 KB

english, 2005

4

Classification of protein complexes based on docking difficulty

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 79 KB

english, 2005

5

CAPRI rounds 3–5 reveal promising successes and future challenges for RosettaDock

Michael D. Daily, David Masica, Arvind Sivasubramanian, Sony Somarouthu, Jeffrey J. Gray

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 195 KB

english, 2005

6

Progress in protein–protein docking: Atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility

Ora Schueler-Furman, Chu Wang, David Baker

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 333 KB

english, 2005

7

Docking to single-domain and multiple-domain proteins: Old and new challenges

E. Ben-Zeev, N. Kowalsman, A. Ben-Shimon, D. Segal, T. Atarot, O. Noivirt, T. Shay, M. Eisenstein

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 249 KB

english, 2005

8

Modeling oligomers with Cn or Dn symmetry: Application to CAPRI target 10

Alexander Berchanski, Dadi Segal, Miriam Eisenstein

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 207 KB

english, 2005

9

ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5

Kevin Wiehe, Brian Pierce, Julian Mintseris, Wei Wei Tong, Robert Anderson, Rong Chen, Zhiping Weng

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 166 KB

english, 2005

10

Protein–protein docking benchmark 2.0: An update

Julian Mintseris, Kevin Wiehe, Brian Pierce, Robert Anderson, Rong Chen, Joël Janin, Zhiping Weng

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 54 KB

english, 2005

11

Approaching the CAPRI challenge with an efficient geometry-based docking

Yuval Inbar, Dina Schneidman-Duhovny, Inbal Halperin, Assaf Oron, Ruth Nussinov, Haim J. Wolfson

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 280 KB

english, 2005

12

Geometry-based flexible and symmetric protein docking

Dina Schneidman-Duhovny, Yuval Inbar, Ruth Nussinov, Haim J. Wolfson

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 803 KB

english, 2005

13

Performance of the first protein docking server ClusPro in CAPRI rounds 3–5

Stephen R. Comeau, Sandor Vajda, Carlos J. Camacho

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 245 KB

english, 2005

14

Modeling side-chains using molecular dynamics improve recognition of binding region in CAPRI targets

Carlos J. Camacho

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 387 KB

english, 2005

15

ATTRACT: Protein–protein docking in CAPRI using a reduced protein model

Martin Zacharias

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 327 KB

english, 2005

16

Study of protein–protein interaction using conformational space annealing

Kyoungrim Lee, Jaehyun Sim, Jooyoung Lee

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 82 KB

english, 2005

17

Incorporation of flexibility into rigid-body docking: Applications in rounds 3–5 of CAPRI

Graham R. Smith, Paul W. Fitzjohn, Christopher S. Page, Paul A. Bates

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 177 KB

english, 2005

18

Docking essential dynamics eigenstructures

Diana Mustard, David W. Ritchie

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 93 KB

english, 2005

19

Scoring docking models with evolutionary information

Michael Tress, David de Juan, Osvaldo Graña, Manuel J. Gómez, Paulino Gómez-Puertas, Jose M. González, Gonzalo López, Alfonso Valencia

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 290 KB

english, 2005

20

Protein–protein docking using 3D-Dock in rounds 3, 4, and 5 of CAPRI

Phil Carter, Victor I. Lesk, Suhail A. Islam, Michael J.E. Sternberg

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 414 KB

english, 2005

21

Searching for protein–protein interaction sites and docking by the methods of molecular dynamics, grid scoring, and the pairwise interaction potential of amino acid residues

Genki Terashi, Mayuko Takeda-Shitaka, Daisuke Takaya, Katsuichiro Komatsu, Hideaki Umeyama

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 248 KB

english, 2005

22

Development and testing of an automated approach to protein docking

Andrei Tovchigrechko, Ilya A. Vakser

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 216 KB

english, 2005

23

Progress in computation and amide hydrogen exchange for prediction of protein–protein complexes

Dennis Law, Matthew Hotchko, Lynn Ten Eyck

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 238 KB

english, 2005

24

Improving CAPRI predictions: Optimized desolvation for rigid-body docking

Juan Fernández-Recio, Ruben Abagyan, Maxim Totrov

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 214 KB

english, 2005

25

Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function

Chi Zhang, Song Liu, Yaoqi Zhou

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 337 KB

english, 2005

26

Biologically enhanced sampling geometric docking and backbone flexibility treatment with multiconformational superposition

Xiao Hui Ma, Chun Hua Li, Long Zhu Shen, Xin Qi Gong, Wei Zu Chen, Cun Xin Wang

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 328 KB

english, 2005

27

Data-driven docking: HADDOCK's adventures in CAPRI

A. D. J. van Dijk, S. J. de Vries, C. Dominguez, H. Chen, H.-X. Zhou, A. M. J. J. Bonvin

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 286 KB

english, 2005