Literature DB >> 22183535

Rosetta Ligand docking with flexible XML protocols.

Gordon Lemmon1, Jens Meiler.   

Abstract

RosettaLigand is premiere software for predicting how a protein and a small molecule interact. Benchmark studies demonstrate that 70% of the top scoring RosettaLigand predicted interfaces are within 2Å RMSD from the crystal structure [1]. The latest release of Rosetta ligand software includes many new features, such as (1) docking of multiple ligands simultaneously, (2) representing ligands as fragments for greater flexibility, (3) redesign of the interface during docking, and (4) an XML script based interface that gives the user full control of the ligand docking protocol.

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Year:  2012        PMID： 22183535      PMCID： PMC3749076          DOI： 10.1007/978-1-61779-465-0_10

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  8 in total

1.  ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility.

Authors:  Jens Meiler; David Baker
Journal:  Proteins       Date:  2006-11-15

2.  RosettaLigand docking with full ligand and receptor flexibility.

Authors:  Ian W Davis; David Baker
Journal:  J Mol Biol       Date:  2008-11-18       Impact factor: 5.469

3.  Blind docking of pharmaceutically relevant compounds using RosettaLigand.

Authors:  Ian W Davis; Kaushik Raha; Martha S Head; David Baker
Journal:  Protein Sci       Date:  2009-09       Impact factor: 6.725

4.  Structure prediction for CASP8 with all-atom refinement using Rosetta.

Authors:  Srivatsan Raman; Robert Vernon; James Thompson; Michael Tyka; Ruslan Sadreyev; Jimin Pei; David Kim; Elizabeth Kellogg; Frank DiMaio; Oliver Lange; Lisa Kinch; Will Sheffler; Bong-Hyun Kim; Rhiju Das; Nick V Grishin; David Baker
Journal:  Proteins       Date:  2009

Review 5.  Practically useful: what the Rosetta protein modeling suite can do for you.

Authors:  Kristian W Kaufmann; Gordon H Lemmon; Samuel L Deluca; Jonathan H Sheehan; Jens Meiler
Journal:  Biochemistry       Date:  2010-04-13       Impact factor: 3.162

6.  Structural determinants of species-selective substrate recognition in human and Drosophila serotonin transporters revealed through computational docking studies.

Authors:  Kristian W Kaufmann; Eric S Dawson; L Keith Henry; Julie R Field; Randy D Blakely; Jens Meiler
Journal:  Proteins       Date:  2009-02-15

7.  Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles.

Authors:  Sidhartha Chaudhury; Jeffrey J Gray
Journal:  J Mol Biol       Date:  2008-05-24       Impact factor: 5.469

8.  De novo computational design of retro-aldol enzymes.

Authors:  Lin Jiang; Eric A Althoff; Fernando R Clemente; Lindsey Doyle; Daniela Röthlisberger; Alexandre Zanghellini; Jasmine L Gallaher; Jamie L Betker; Fujie Tanaka; Carlos F Barbas; Donald Hilvert; Kendall N Houk; Barry L Stoddard; David Baker
Journal:  Science       Date:  2008-03-07       Impact factor: 47.728
  8 in total
  54 in total

1.  Protein-small molecule docking with receptor flexibility in iMOLSDOCK.

Authors:  D Sam Paul; N Gautham
Journal:  J Comput Aided Mol Des       Date:  2018-08-20       Impact factor: 3.686

2.  Probing the metabotropic glutamate receptor 5 (mGlu₅) positive allosteric modulator (PAM) binding pocket: discovery of point mutations that engender a "molecular switch" in PAM pharmacology.

Authors:  Karen J Gregory; Elizabeth D Nguyen; Sean D Reiff; Emma F Squire; Shaun R Stauffer; Craig W Lindsley; Jens Meiler; P Jeffrey Conn
Journal:  Mol Pharmacol       Date:  2013-02-26       Impact factor: 4.436

3.  Identification of specific ligand-receptor interactions that govern binding and cooperativity of diverse modulators to a common metabotropic glutamate receptor 5 allosteric site.

Authors:  Karen J Gregory; Elizabeth D Nguyen; Chrysa Malosh; Jeffrey L Mendenhall; Jessica Z Zic; Brittney S Bates; Meredith J Noetzel; Emma F Squire; Eric M Turner; Jerri M Rook; Kyle A Emmitte; Shaun R Stauffer; Craig W Lindsley; Jens Meiler; P Jeffrey Conn
Journal:  ACS Chem Neurosci       Date:  2014-02-26       Impact factor: 4.418

4.  Atomic structures of corkscrew-forming segments of SOD1 reveal varied oligomer conformations.

Authors:  Smriti Sangwan; Michael R Sawaya; Kevin A Murray; Michael P Hughes; David S Eisenberg
Journal:  Protein Sci       Date:  2018-03-10       Impact factor: 6.725

5.  Structural mechanisms underlying activation of TRPV1 channels by pungent compounds in gingers.

Authors:  Yue Yin; Yawen Dong; Simon Vu; Fan Yang; Vladimir Yarov-Yarovoy; Yuhua Tian; Jie Zheng
Journal:  Br J Pharmacol       Date:  2019-07-22       Impact factor: 8.739

6.  Exploration of allosteric agonism structure-activity relationships within an acetylene series of metabotropic glutamate receptor 5 (mGlu5) positive allosteric modulators (PAMs): discovery of 5-((3-fluorophenyl)ethynyl)-N-(3-methyloxetan-3-yl)picolinamide (ML254).

Authors:  Mark Turlington; Meredith J Noetzel; Aspen Chun; Ya Zhou; Rocco D Gogliotti; Elizabeth D Nguyen; Karen J Gregory; Paige N Vinson; Jerri M Rook; Kiran K Gogi; Zixiu Xiang; Thomas M Bridges; J Scott Daniels; Carrie Jones; Colleen M Niswender; Jens Meiler; P Jeffrey Conn; Craig W Lindsley; Shaun R Stauffer
Journal:  J Med Chem       Date:  2013-10-09       Impact factor: 7.446

7.  Active Site Flexibility as a Hallmark for Efficient PET Degradation by I. sakaiensis PETase.

Authors:  Tobias Fecker; Pablo Galaz-Davison; Felipe Engelberger; Yoshie Narui; Marcos Sotomayor; Loreto P Parra; César A Ramírez-Sarmiento
Journal:  Biophys J       Date:  2018-03-27       Impact factor: 4.033

8.  Benchmarking GPCR homology model template selection in combination with de novo loop generation.

Authors:  Gregory L Szwabowski; Paige N Castleman; Chandler K Sears; Lee H Wink; Judith A Cole; Daniel L Baker; Abby L Parrill
Journal:  J Comput Aided Mol Des       Date:  2020-07-31       Impact factor: 3.686

9.  α2A- and α2C-Adrenoceptors as Potential Targets for Dopamine and Dopamine Receptor Ligands.

Authors:  Marta Sánchez-Soto; Verònica Casadó-Anguera; Hideaki Yano; Brian Joseph Bender; Ning-Sheng Cai; Estefanía Moreno; Enric I Canela; Antoni Cortés; Jens Meiler; Vicent Casadó; Sergi Ferré
Journal:  Mol Neurobiol       Date:  2018-03-18       Impact factor: 5.590

10.  BCL::MolAlign: Three-Dimensional Small Molecule Alignment for Pharmacophore Mapping.

Authors:  Benjamin P Brown; Jeffrey Mendenhall; Jens Meiler
Journal:  J Chem Inf Model       Date:  2019-02-12       Impact factor: 4.956
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