Literature DB >> 11134930

A number of real-space torsion-angle refinement techniques for proteins, nucleic acids, ligands and solvent.

T J Oldfield1.   

Abstract

This paper describes the implementation of real-space torsion-angle refinement as a tool for model (re)building. The algorithmic details and parameterization for a number of different protocols are presented, as well as the handling of special conditions. Examples illustrating the use of the algorithms show that these tools provide a great advantage over traditional methods for building macromolecular structures. All these algorithms have been implemented in QUANTA (MSI), currently available as version QUANTA98.

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Year:  2001        PMID: 11134930     DOI: 10.1107/s0907444900014098

Source DB:  PubMed          Journal:  Acta Crystallogr D Biol Crystallogr        ISSN: 0907-4449


  22 in total

1.  Improved affinity of engineered streptavidin for the Strep-tag II peptide is due to a fixed open conformation of the lid-like loop at the binding site.

Authors:  Ingo P Korndörfer; Arne Skerra
Journal:  Protein Sci       Date:  2002-04       Impact factor: 6.725

2.  Crystal structure of archaeal chromatin protein Alba2-double-stranded DNA complex from Aeropyrum pernix K1.

Authors:  Tomoyuki Tanaka; Sivaraman Padavattan; Thirumananseri Kumarevel
Journal:  J Biol Chem       Date:  2012-02-10       Impact factor: 5.157

3.  Crystal structure of LpxC from Pseudomonas aeruginosa complexed with the potent BB-78485 inhibitor.

Authors:  Igor Mochalkin; John D Knafels; Sandra Lightle
Journal:  Protein Sci       Date:  2008-03       Impact factor: 6.725

4.  A new crystal form of human tear lipocalin reveals high flexibility in the loop region and induced fit in the ligand cavity.

Authors:  Daniel A Breustedt; Lorenz Chatwell; Arne Skerra
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-09-16

5.  Q|R: quantum-based refinement.

Authors:  Min Zheng; Jeffrey R Reimers; Mark P Waller; Pavel V Afonine
Journal:  Acta Crystallogr D Struct Biol       Date:  2017-01-01       Impact factor: 7.652

6.  Assessing protein conformational sampling methods based on bivariate lag-distributions of backbone angles.

Authors:  Mehdi Maadooliat; Xin Gao; Jianhua Z Huang
Journal:  Brief Bioinform       Date:  2012-08-27       Impact factor: 11.622

7.  A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry.

Authors:  Oleg V Sobolev; Pavel V Afonine; Nigel W Moriarty; Maarten L Hekkelman; Robbie P Joosten; Anastassis Perrakis; Paul D Adams
Journal:  Structure       Date:  2020-08-27       Impact factor: 5.006

8.  Characterization of substrate binding and catalysis in the potential antibacterial target N-acetylglucosamine-1-phosphate uridyltransferase (GlmU).

Authors:  Igor Mochalkin; Sandra Lightle; Yaqi Zhu; Jeffrey F Ohren; Cindy Spessard; Nickolay Y Chirgadze; Craig Banotai; Michael Melnick; Laura McDowell
Journal:  Protein Sci       Date:  2007-12       Impact factor: 6.725

9.  Structure of a small-molecule inhibitor complexed with GlmU from Haemophilus influenzae reveals an allosteric binding site.

Authors:  Igor Mochalkin; Sandra Lightle; Lakshmi Narasimhan; Dirk Bornemeier; Michael Melnick; Steven Vanderroest; Laura McDowell
Journal:  Protein Sci       Date:  2008-01-24       Impact factor: 6.725

10.  ST1710-DNA complex crystal structure reveals the DNA binding mechanism of the MarR family of regulators.

Authors:  Thirumananseri Kumarevel; Tomoyuki Tanaka; Takashi Umehara; Shigeyuki Yokoyama
Journal:  Nucleic Acids Res       Date:  2009-06-09       Impact factor: 16.971

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