Protein Structure Prediction, Mohammed Zaki; Chris Bystroff

Автор: Ying Xu; Dong Xu; Jie Liang
Название: Computational Methods for Protein Structure Prediction and Modeling
ISBN: 1441922059 ISBN-13(EAN): 9781441922052
Издательство: Springer
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Описание: Volume One of this two-volume sequence focuses on the basic characterization of known protein structures, and structure prediction from protein sequence information. Eleven chapters survey of the field, covering key topics in modeling, force fields, classification, computational methods, and structure prediction.

Автор: G.D. Fasman
Название: Prediction of Protein Structure and the Principles of Protein Conformation
ISBN: 0306431319 ISBN-13(EAN): 9780306431319
Издательство: Springer
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Автор: Daisuke Kihara
Название: Protein Structure Prediction
ISBN: 1493944614 ISBN-13(EAN): 9781493944613
Издательство: Springer
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Цена: 14673.00 р.
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Описание:

1. Protein Structure Modeling with MODELLER

Benjamin Webb, Andrej Sali

2. RaptorX Server: A Resource for Template-based Protein Structure Modeling

Morten Kдllberg, 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, Josй 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

Автор: Yaoqi Zhou; Andrzej Kloczkowski; Eshel Faraggi; Yu
Название: Prediction of Protein Secondary Structure
ISBN: 1493964046 ISBN-13(EAN): 9781493964048
Издательство: Springer
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Цена: 20962.00 р.
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Описание: This thorough volume explores predicting one-dimensional functional properties, functional sites in particular, from protein sequences, an area which is getting more and more attention. Beginning with secondary structure prediction based on sequence only, the book continues by exploring secondary structure prediction based on evolution information, prediction of solvent accessible surface areas and backbone torsion angles, model building, global structural properties, functional properties, as well as visualizing interior and protruding regions in proteins. Written for the highly successful Methods in Molecular Biology series, the chapters include the kind of detail and implementation advice to ensure success in the laboratory.

Автор: Daisuke Kihara
Название: Protein Structure Prediction
ISBN: 1493903659 ISBN-13(EAN): 9781493903658
Издательство: Springer
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Автор: Neocles Leontis; Eric Westhof
Название: RNA 3D Structure Analysis and Prediction
ISBN: 3642445691 ISBN-13(EAN): 9783642445699
Издательство: Springer
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Цена: 26120.00 р.
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Описание: This volume provides a comprehensive overview of current progress in the field by leading practitioners employing a variety of methods to model RNA 3D structures by homology, by fragment assembly, and by de novo energy and knowledge-based approaches.

Автор: Hou, Jingyu
Название: New Approaches of Protein Function Prediction from Protein Intera
ISBN: 0128098147 ISBN-13(EAN): 9780128098141
Издательство: Elsevier Science
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Описание:

New Approaches of Protein Function Prediction from Protein Interaction Networks contains the critical aspects of PPI network based protein function prediction, including semantically assessing the reliability of PPI data, measuring the functional similarity between proteins, dynamically selecting prediction domains, predicting functions, and establishing corresponding prediction frameworks.

Автор: Ying Xu; Dong Xu; Jie Liang
Название: Computational Methods for Protein Structure Prediction and Modeling
ISBN: 1441922067 ISBN-13(EAN): 9781441922069
Издательство: Springer
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Описание: Volume Two of this two-volume sequence presents a comprehensive overview of protein structure prediction methods and includes protein threading, De novo methods, applications to membrane proteins and protein complexes, structure-based drug design, as well as structure prediction as a systems problem.

Автор: G.D. Fasman
Название: Prediction of Protein Structure and the Principles of Protein Conformation
ISBN: 1461288606 ISBN-13(EAN): 9781461288602
Издательство: Springer
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Цена: 28732.00 р.
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Автор: Daisuke Kihara
Название: Protein Function Prediction for Omics Era
ISBN: 9400799640 ISBN-13(EAN): 9789400799646
Издательство: Springer
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Цена: 28732.00 р.
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Описание: This book examines the emerging development of computational gene function prediction methods, which are targeted to analyze large scale data, and also those which use such omics data as additional source of function prediction.

Автор: Daisuke Kihara
Название: Protein Function Prediction
ISBN: 1493970135 ISBN-13(EAN): 9781493970131
Издательство: Springer
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Цена: 19564.00 р.
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Описание: Preface...
Table of Contents...
Contributing Authors...

1. Using PFP and ESG Protein Function Prediction Web Servers
Qing Wei, Joshua McGraw, Ishita Khan, and Daisuke Kihara

2. GHOSTX: A Fast Sequence Homology Search Tool for Functional Annotation of Metagenomic Data
Shuji Suzuki, Takashi Ishida, Masahito Ohue, Masanori Kakuta, and Yutaka Akiyama

3. From Gene Annotation to Function Prediction for Metagenomics
Fatemeh Sharifi and Yuzhen Ye

4. An Agile Functional Analysis of Metagenomic Data using SUPER-FOCUS
Genivaldo Gueiros Z. Silva, Fabyano A. C. Lopes, and Robert A. Edwards

5. MPFit: Computational Tool for Predicting Moonlighting Proteins
Ishita Khan, Joshua McGraw, and Daisuke Kihara

6. Predicting Secretory Proteins with SignalP
Henrik Nielsen

7. The ProFunc Function Prediction Server
Roman A. Laskowski

8. G-LoSA for Prediction of Protein-Ligand Binding Sites and Structures
Hui Sun Lee and Wonpil Im

9. Local Alignment of Ligand Binding Sites in Proteins for Polypharmacology and Drug Repositioning
Michal Brylinski

10. WATsite2.0 with PyMOL Plugin: Hydration Site Prediction and Visualization
Ying Yang, Bingjie Hu, and Markus A. Lill

11. Enzyme Annotation and Metabolic Reconstruction Using KEGG
Minoru Kanehisa

12. Ortholog Identification and Comparative Analysis of Microbial Genomes using MBGD and RECOG
Ikuo Uchiyama

13. Exploring Protein Function Using the Saccharomyces Genome Database
Edith D. Wong

14. Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates using MouseNet Server
Eiru Kim and Insuk Lee

15. The FANTOM5 Computation Ecosystem: Genomic Information Hub for Promoters and Active Enhancers
Imad Abugessaisa, Shuhei Noguchi, Piero Carninci, and Takeya Kasukawa

16. Multi-Algorithm Particle Simulations with Spatiocyte
Satya N. V. Arjunan and Koichi Takahashi

Автор: N. Rama Krishna; Lawrence J. Berliner
Название: Structure Computation and Dynamics in Protein NMR
ISBN: 0306459531 ISBN-13(EAN): 9780306459535
Издательство: Springer
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Цена: 44582.00 р.
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Описание: Covers the developments in molecular modeling on the basis of spectroscopic or diffraction data, pulse sequences and computational methods for automated assignment and structure determination, structure calculation of symmetric oligomer proteins, and structure refinement by hybrid-hybrid matrix method from 3D NOESY-NOESY data.