Preface ......................................................... v
Contributors ................................................... ix
1 Protein Structure Modeling with MODELLER ..................... 1
Benjamin Webb and Andrej Sali
2 RaptorX server: A Resource for Template-Based Protein
Structure Modeling .......................................... 17
Morten Källberg, Gobar Margaryan, Sheng Wang, Jianzhu Ma,
and Jinbo Xu
3 The MULTICOM Protein Tertiary Structure Prediction System ... 29
Jilong Li, Debswapna Bbattacharya, Renzhi Cao, Badri
Adhikari, Xin Deng, Jesse Eickholt, and Jianlin Cheng
4 Modeling of Protein Side-Chain Conformations with RASP ...... 43
Zhichao Miao, Tang Cao, and Taijiao Jiang
5 Direct Coupling Analysis for Protein Contact Prediction ..... 55
Faruck Morcos, Terence Hwa, José N. Onuchic, and Martin
Weigt
6 ITScorePro: An Efficient Scoring Program for Evaluating
the Energy Scores of Protein Structures for Structure
Prediction .................................................. 71
Sheng-You Huang and Xiaoqin Zou
7 Assessing the Quality of Modelled 3D Protein Structures
Using the ModFOLD Server .................................... 83
Daniel Barry Roche, Maria Teresa Buenavista, and Liam
James McGujfin
8 3D-SURFER 2.0: Web Platform for Real-Time Search
and Characterization of Protein Surfaces ................... 105
Yi Xiong, Juan Esquivel-Rodriguez, Lee Sael, and Daisuke
Kihara
9 SPOT-Seq-RNA: Predicting Protein-RNA Complex Structure
and RNA-Binding Function by Fold Recognition and Binding
Affinity Prediction ........................................ 119
Yuedong Yang, Huiying Zhao, Jihua Wang, and Yaoqi Zhou
10 POODLE: Tools Predicting Intrinsically Disordered Regions
of Amino Acid Sequence ..................................... 131
Каnа Shimizu
11 Prediction of Intrinsic Disorder in Proteins Using MFDp2 ... 147
Marcin J. Mizianty, Vladimir Uversky, and Lukasz Kurgan
12 Modeling Protein-Protein Complexes Using the HADDOCK
Webserver "Modeling Protein Complexes with HADDOCK" ........ 163
Gydo C.P. van Zundert and Alexandre M.J.J. Bonvin
13 Predicting the Structure of Protein-Protein Complexes
Using the SwarmDock Web Server ............................. 181
Mieczyslaw Torchala and Paul A. Bates
14 DOCK/PIERR: Web Server for Structure Prediction of
Protein-Protein Complexes .................................. 199
Shruthi Viswanath, D.V.S. Ravikant, and Ron Elber
15 Pairwise and Multimeric Protein-Protein Docking
Using the LZerD Program Suite .............................. 209
Juan Esquivel-Rodriguez, Vianney Filos-Gonzalez, Bin Li,
and Daisuke Kihara
16 Protocols for Efficient Simulations of Long-Time Protein
Dynamics Using Coarse-Grained CABS Model ................... 235
Michal Jamroz, Andrzej Kolinski, and Sebastian Kmiecik
Index ......................................................... 257
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