Protein Structure Prediction

ISBN-13: 9781493944613 / Angielski / Miękka / 2016 / 253 str.

Daisuke Kihara

Opis

Protein Structure Prediction, Third Edition expands on previous editions by focusing on software and web servers. With new chapters that provide instructions on how to use a computational method with examples of prediction by the method. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible protocols, and key tips on troubleshooting and avoiding known pitfalls.Authoritative and cutting-edge, Protein Structure Prediction, Third Edition provides diverse methods detailing the expansion of the computational protein structure prediction field.

Spis treści

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