1. Protein Structure Modeling with MODELLER
Benjamin Webb, Andrej Sali
2. RaptorX Server: A Resource for Template-based Protein Structure Modeling
Morten Källberg, Gohar Margaryan, Sheng Wang, Jianzhu Ma and Jinbo Xu
3. The MULTICOM Protein Tertiary Structure Prediction System
Jilong Li, Debswapna Bhattacharya, Renzhi Cao, Badri Adhikari, Xin Deng, Jesse Eickholt and Jianlin Cheng
4. Modeling of Protein Side-chain Conformations with RASP
Miao Zhichao, Cao Yang and Jiang Taijiao
5. Direct Coupling Analysis for Protein Contact Prediction
Faruck Morcos, Terence Hwa, José N. Onuchic, Martin Weigt
6. ITScorePro - An Efficient Scoring Program for Evaluating the Energy Scores of Protein Structures for Structure Prediction
Sheng-You Huang and Xiaoqin Zou
7. Assessing the Quality of Modelled 3D Protein Structures using the ModFOLD Server
Daniel Barry Roche, Maria Teresa Buenavista, and Liam James McGuffin
8. 3D-SURFER 2.0: Web Platform for Real-Time Search and Characterization of Protein Surfaces 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
Yuedong Yang, Huiying Zhao, Jihua Wang and Yaoqi Zhou
10. POODLE: Tools Predicting Intrinsically Disordered Regions of Amino Acid Sequence
Kana Shimizu
11. Prediction of Intrinsic Disorder in Proteins using MFDp2
Marcin J Mizianty, Vladimir Uversky and Lukasz Kurgan
12. Modeling protein-protein Complexes using the HADDOCK Webserver
G.C.P. van Zundert, and A.M.J.J. Bonvin
13. Predicting the Structure of Protein-protein Complexes using the SwarmDock Web Server
Mieczyslaw Torchala and Paul A. Bates
14. DOCK/PIERR: Web Server for Structure Prediction of Protein--Protein Complexes
S Viswanath, D.V.S. Ravikant and R Elber
15. Pairwise and Multimeric Protein-Protein Docking Using the LZerD Program Suite
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
Michal Jamroz, Andrzej Kolinski, Sebastian Kmiecik
