Literature DB >> 19644455

Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling.

Daniel J Mandell, Evangelos A Coutsias, Tanja Kortemme.   

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Year:  2009        PMID： 19644455      PMCID： PMC2847683          DOI： 10.1038/nmeth0809-551

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


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  5 in total

1.  Cyclic coordinate descent: A robotics algorithm for protein loop closure.

Authors:  Adrian A Canutescu; Roland L Dunbrack
Journal:  Protein Sci       Date:  2003-05       Impact factor: 6.725

Review 2.  Progress in modeling of protein structures and interactions.

Authors:  Ora Schueler-Furman; Chu Wang; Phil Bradley; Kira Misura; David Baker
Journal:  Science       Date:  2005-10-28       Impact factor: 47.728

3.  Protein-protein docking with backbone flexibility.

Authors:  Chu Wang; Philip Bradley; David Baker
Journal:  J Mol Biol       Date:  2007-08-02       Impact factor: 5.469

4.  Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling.

Authors:  Anthony K Felts; Emilio Gallicchio; Dmitriy Chekmarev; Kristina A Paris; Richard A Friesner; Ronald M Levy
Journal:  J Chem Theory Comput       Date:  2008       Impact factor: 6.006

5.  Toward better refinement of comparative models: predicting loops in inexact environments.

Authors:  Benjamin D Sellers; Kai Zhu; Suwen Zhao; Richard A Friesner; Matthew P Jacobson
Journal:  Proteins       Date:  2008-08-15
  5 in total
  208 in total

1.  Protein loop closure using orientational restraints from NMR data.

Authors:  Chittaranjan Tripathy; Jianyang Zeng; Pei Zhou; Bruce Randall Donald
Journal:  Proteins       Date:  2011-12-13

2.  Predicting flexible loop regions that interact with ligands: the challenge of accurate scoring.

Authors:  Matthew L Danielson; Markus A Lill
Journal:  Proteins       Date:  2011-11-09

3.  Modeling large regions in proteins: applications to loops, termini, and folding.

Authors:  Aashish N Adhikari; Jian Peng; Michael Wilde; Jinbo Xu; Karl F Freed; Tobin R Sosnick
Journal:  Protein Sci       Date:  2011-12-05       Impact factor: 6.725

4.  An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling.

Authors:  Parin Sripakdeevong; Wipapat Kladwang; Rhiju Das
Journal:  Proc Natl Acad Sci U S A       Date:  2011-12-05       Impact factor: 11.205

5.  Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair.

Authors:  Gregory T Kapp; Sen Liu; Amelie Stein; Derek T Wong; Attila Reményi; Brian J Yeh; James S Fraser; Jack Taunton; Wendell A Lim; Tanja Kortemme
Journal:  Proc Natl Acad Sci U S A       Date:  2012-03-07       Impact factor: 11.205

6.  A fluorogenic red fluorescent protein heterodimer.

Authors:  Spencer C Alford; Ahmed S Abdelfattah; Yidan Ding; Robert E Campbell
Journal:  Chem Biol       Date:  2012-03-23

7.  Mapping the interaction site for a β-scorpion toxin in the pore module of domain III of voltage-gated Na(+) channels.

Authors:  Joel Z Zhang; Vladimir Yarov-Yarovoy; Todd Scheuer; Izhar Karbat; Lior Cohen; Dalia Gordon; Michael Gurevitz; William A Catterall
Journal:  J Biol Chem       Date:  2012-07-02       Impact factor: 5.157

8.  Protein loop modeling by using fragment assembly and analytical loop closure.

Authors:  Julian Lee; Dongseon Lee; Hahnbeom Park; Evangelos A Coutsias; Chaok Seok
Journal:  Proteins       Date:  2010-09-24

9.  Ligand-mimicking receptor variant discloses binding and activation mode of prolactin-releasing peptide.

Authors:  Daniel Rathmann; Diana Lindner; Stephanie H DeLuca; Kristian W Kaufmann; Jens Meiler; Annette G Beck-Sickinger
Journal:  J Biol Chem       Date:  2012-07-09       Impact factor: 5.157

10.  InteractiveROSETTA: a graphical user interface for the PyRosetta protein modeling suite.

Authors:  Christian D Schenkelberg; Christopher Bystroff
Journal:  Bioinformatics       Date:  2015-08-26       Impact factor: 6.937
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