Literature DB >> 27322406

Comparative Protein Structure Modeling Using MODELLER.

Benjamin Webb1, Andrej Sali1.   

Abstract

Comparative protein structure modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and how to use the ModBase database of such models, and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described. © 2016 by John Wiley & Sons, Inc.
Copyright © 2016 John Wiley & Sons, Inc.

Entities:  

Keywords:  MODELLER; ModBase; comparative modeling; protein fold; protein structure; structure prediction

Mesh：

Substances：

Year:  2016        PMID： 27322406      PMCID： PMC5031415          DOI： 10.1002/cpbi.3

Source DB:  PubMed          Journal:  Curr Protoc Bioinformatics        ISSN： 1934-3396


  222 in total

1.  lynx1, an endogenous toxin-like modulator of nicotinic acetylcholine receptors in the mammalian CNS.

Authors:  J M Miwa; I Ibanez-Tallon; G W Crabtree; R Sánchez; A Sali; L W Role; N Heintz
Journal:  Neuron       Date:  1999-05       Impact factor: 17.173

2.  Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the Surface Generalized Born solvent model.

Authors:  Anthony K Felts; Emilio Gallicchio; Anders Wallqvist; Ronald M Levy
Journal:  Proteins       Date:  2002-08-01

3.  A hierarchical approach to all-atom protein loop prediction.

Authors:  Matthew P Jacobson; David L Pincus; Chaya S Rapp; Tyler J F Day; Barry Honig; David E Shaw; Richard A Friesner
Journal:  Proteins       Date:  2004-05-01

4.  Application of molecular dynamics with interproton distance restraints to three-dimensional protein structure determination. A model study of crambin.

Authors:  G M Clore; A T Brünger; M Karplus; A M Gronenborn
Journal:  J Mol Biol       Date:  1986-10-05       Impact factor: 5.469

5.  Convergent evolution of Trichomonas vaginalis lactate dehydrogenase from malate dehydrogenase.

Authors:  G Wu; A Fiser; B ter Kuile; A Sali; M Müller
Journal:  Proc Natl Acad Sci U S A       Date:  1999-05-25       Impact factor: 11.205

6.  FoXS: a web server for rapid computation and fitting of SAXS profiles.

Authors:  Dina Schneidman-Duhovny; Michal Hammel; Andrej Sali
Journal:  Nucleic Acids Res       Date:  2010-05-27       Impact factor: 16.971

7.  Large-scale protein structure modeling of the Saccharomyces cerevisiae genome.

Authors:  R Sánchez; A Sali
Journal:  Proc Natl Acad Sci U S A       Date:  1998-11-10       Impact factor: 11.205

8.  Study of the structural dynamics of the E coli 70S ribosome using real-space refinement.

Authors:  Haixiao Gao; Jayati Sengupta; Mikel Valle; Andrei Korostelev; Narayanan Eswar; Scott M Stagg; Patrick Van Roey; Rajendra K Agrawal; Stephen C Harvey; Andrej Sali; Michael S Chapman; Joachim Frank
Journal:  Cell       Date:  2003-06-13       Impact factor: 41.582

9.  ModBase, a database of annotated comparative protein structure models, and associated resources.

Authors:  Ursula Pieper; Benjamin M Webb; David T Barkan; Dina Schneidman-Duhovny; Avner Schlessinger; Hannes Braberg; Zheng Yang; Elaine C Meng; Eric F Pettersen; Conrad C Huang; Ruchira S Datta; Parthasarathy Sampathkumar; Mallur S Madhusudhan; Kimmen Sjölander; Thomas E Ferrin; Stephen K Burley; Andrej Sali
Journal:  Nucleic Acids Res       Date:  2010-11-19       Impact factor: 16.971

10.  The SWISS-MODEL Repository and associated resources.

Authors:  Florian Kiefer; Konstantin Arnold; Michael Künzli; Lorenza Bordoli; Torsten Schwede
Journal:  Nucleic Acids Res       Date:  2008-10-18       Impact factor: 16.971
View more
  546 in total

1.  Molecular Interaction between Distal C-Terminal Domain of the CB1 Cannabinoid Receptor and Cannabinoid Receptor Interacting Proteins (CRIP1a/CRIP1b).

Authors:  Pratishtha Singh; Anjali Ganjiwale; Allyn C Howlett; Sudha M Cowsik
Journal:  J Chem Inf Model       Date:  2019-12-10       Impact factor: 4.956

2.  Specific binding between Bacillus thuringiensis Cry9Aa and Vip3Aa toxins synergizes their toxicity against Asiatic rice borer (Chilo suppressalis).

Authors:  Zeyu Wang; Longfa Fang; Zishan Zhou; Sabino Pacheco; Isabel Gómez; Fuping Song; Mario Soberón; Jie Zhang; Alejandra Bravo
Journal:  J Biol Chem       Date:  2018-06-01       Impact factor: 5.157

3.  A chemical inhibitor of heat shock protein 78 (HSP78) from Leishmania donovani represents a potential antileishmanial drug candidate.

Authors:  Sonali Das; Anindyajit Banerjee; Mohd Kamran; Sarfaraz Ahmad Ejazi; Mohammad Asad; Nahid Ali; Saikat Chakrabarti
Journal:  J Biol Chem       Date:  2020-05-29       Impact factor: 5.157

4.  Functional diversification of the NleG effector family in enterohemorrhagic Escherichia coli.

Authors:  Dylan Valleau; Dustin J Little; Dominika Borek; Tatiana Skarina; Andrew T Quaile; Rosa Di Leo; Scott Houliston; Alexander Lemak; Cheryl H Arrowsmith; Brian K Coombes; Alexei Savchenko
Journal:  Proc Natl Acad Sci U S A       Date:  2018-09-14       Impact factor: 11.205

5.  Production of Galactose Oxidase Inside the Fusarium fujikuroi Species Complex and Recombinant Expression and Characterization of the Galactose Oxidase GaoA Protein from Fusarium subglutinans.

Authors:  Carla Bertechini Faria; Fausto Fernandes de Castro; Damaris Batistão Martim; Camila Agnes Lumi Abe; Kelly Valério Prates; Marco Aurelio Schuler de Oliveira; Ione Parra Barbosa-Tessmann
Journal:  Mol Biotechnol       Date:  2019-09       Impact factor: 2.695

6.  Species Specificity of Vaccinia Virus Complement Control Protein for the Bovine Classical Pathway Is Governed Primarily by Direct Interaction of Its Acidic Residues with Factor I.

Authors:  Jitendra Kumar; Viveka Nand Yadav; Swastik Phulera; Ashish Kamble; Avneesh Kumar Gautam; Hemendra Singh Panwar; Arvind Sahu
Journal:  J Virol       Date:  2017-09-12       Impact factor: 5.103

7.  Differential Roles of Extracellular Histidine Residues of GPR68 for Proton-Sensing and Allosteric Modulation by Divalent Metal Ions.

Authors:  Xi-Ping Huang; Terrence P Kenakin; Shuo Gu; Brian K Shoichet; Bryan L Roth
Journal:  Biochemistry       Date:  2020-09-10       Impact factor: 3.162

Review 8.  A Systematic Literature Review of Whole Exome and Genome Sequencing Population Studies of Genetic Susceptibility to Cancer.

Authors:  Alisa M Goldstein; Elizabeth M Gillanders; Melissa Rotunno; Rolando Barajas; Mindy Clyne; Elise Hoover; Naoko I Simonds; Tram Kim Lam; Leah E Mechanic
Journal:  Cancer Epidemiol Biomarkers Prev       Date:  2020-05-28       Impact factor: 4.254

9.  A Chemical Probe for Dark Kinase STK17B Derives Its Potency and High Selectivity through a Unique P-Loop Conformation.

Authors:  Alfredo Picado; Apirat Chaikuad; Carrow I Wells; Safal Shrestha; William J Zuercher; Julie E Pickett; Frank E Kwarcinski; Parvathi Sinha; Chandi S de Silva; Reena Zutshi; Shubin Liu; Natarajan Kannan; Stefan Knapp; David H Drewry; Timothy M Willson
Journal:  J Med Chem       Date:  2020-11-20       Impact factor: 7.446

10.  Single-channel properties of skeletal muscle ryanodine receptor pore Δ4923FF4924 in two brothers with a lethal form of fetal akinesia.

Authors:  Le Xu; Frederike L Harms; Venkat R Chirasani; Daniel A Pasek; Fanny Kortüm; Peter Meinecke; Nikolay V Dokholyan; Kerstin Kutsche; Gerhard Meissner
Journal:  Cell Calcium       Date:  2020-02-17       Impact factor: 6.817
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.