Literature DB >> 7876901

Flexibases: a way to enhance the use of molecular docking methods.

S K Kearsley1, D J Underwood, R P Sheridan, M D Miller.   

Abstract

Specially expanded databases containing three-dimensional structures are created to enhance the utility of docking methods to find new leads, i.e., active compounds of pharmacological interest. The expansion is based on the automatic generation of a set of maximally dissimilar conformations. The ligand receptor system of methotrexate and dihydrofolate reductase is used to demonstrate the feasibility of creating flexibases and their utility in docking studies.

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Year:  1994        PMID： 7876901     DOI： 10.1007/bf00123666

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN： 0920-654X            Impact factor:   3.686


  20 in total

1.  Sampling and efficiency of metric matrix distance geometry: a novel partial metrization algorithm.

Authors:  J Kuszewski; M Nilges; A T Brünger
Journal:  J Biomol NMR       Date:  1992-01       Impact factor: 2.835

2.  CLIX: a search algorithm for finding novel ligands capable of binding proteins of known three-dimensional structure.

Authors:  M C Lawrence; P C Davis
Journal:  Proteins       Date:  1992-01

Review 3.  Structure-based strategies for drug design and discovery.

Authors:  I D Kuntz
Journal:  Science       Date:  1992-08-21       Impact factor: 47.728

4.  The computer program LUDI: a new method for the de novo design of enzyme inhibitors.

Authors:  H J Böhm
Journal:  J Comput Aided Mol Des       Date:  1992-02       Impact factor: 3.686

5.  Automated site-directed drug design using molecular lattices.

Authors:  R A Lewis; D C Roe; C Huang; T E Ferrin; R Langridge; I D Kuntz
Journal:  J Mol Graph       Date:  1992-06

6.  Docking flexible ligands to macromolecular receptors by molecular shape.

Authors:  R L DesJarlais; R P Sheridan; J S Dixon; I D Kuntz; R Venkataraghavan
Journal:  J Med Chem       Date:  1986-11       Impact factor: 7.446

7.  Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure.

Authors:  R L DesJarlais; R P Sheridan; G L Seibel; J S Dixon; I D Kuntz; R Venkataraghavan
Journal:  J Med Chem       Date:  1988-04       Impact factor: 7.446

8.  A geometric approach to macromolecule-ligand interactions.

Authors:  I D Kuntz; J M Blaney; S J Oatley; R Langridge; T E Ferrin
Journal:  J Mol Biol       Date:  1982-10-25       Impact factor: 5.469

9.  Influence of environment on the antifolate drug trimethoprim: energy minimization studies.

Authors:  C L Fisher; V A Roberts; A T Hagler
Journal:  Biochemistry       Date:  1991-04-09       Impact factor: 3.162

10.  Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. II. Environment of bound NADPH and implications for catalysis.

Authors:  D J Filman; J T Bolin; D A Matthews; J Kraut
Journal:  J Biol Chem       Date:  1982-11-25       Impact factor: 5.157
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  15 in total

1.  DREAM++: flexible docking program for virtual combinatorial libraries.

Authors:  S Makino; T J Ewing; I D Kuntz
Journal:  J Comput Aided Mol Des       Date:  1999-09       Impact factor: 3.686

2.  Comparison of two implementations of the incremental construction algorithm in flexible docking of thrombin inhibitors.

Authors:  R M Knegtel; D M Bayada; R A Engh; W von der Saal; V J van Geerestein; P D Grootenhuis
Journal:  J Comput Aided Mol Des       Date:  1999-03       Impact factor: 3.686

3.  FLASHFLOOD: a 3D field-based similarity search and alignment method for flexible molecules.

Authors:  M C Pitman; W K Huber; H Horn; A Krämer; J E Rice; W C Swope
Journal:  J Comput Aided Mol Des       Date:  2001-07       Impact factor: 3.686

4.  Can we separate active from inactive conformations?

Authors:  David J Diller; Kenneth M Merz
Journal:  J Comput Aided Mol Des       Date:  2002-02       Impact factor: 3.686

5.  Fast 3D molecular superposition and similarity search in databases of flexible molecules.

Authors:  Andreas Krämer; Hans W Horn; Julia E Rice
Journal:  J Comput Aided Mol Des       Date:  2003-01       Impact factor: 3.686

6.  Comparative study of several algorithms for flexible ligand docking.

Authors:  Badry D Bursulaya; Maxim Totrov; Ruben Abagyan; Charles L Brooks
Journal:  J Comput Aided Mol Des       Date:  2003-11       Impact factor: 3.686

7.  Docking validation resources: protein family and ligand flexibility experiments.

Authors:  Sudipto Mukherjee; Trent E Balius; Robert C Rizzo
Journal:  J Chem Inf Model       Date:  2010-10-29       Impact factor: 4.956

8.  Empirical regioselectivity models for human cytochromes P450 3A4, 2D6, and 2C9.

Authors:  Robert P Sheridan; Kenneth R Korzekwa; Rhonda A Torres; Matthew J Walker
Journal:  J Med Chem       Date:  2007-06-19       Impact factor: 7.446

9.  An inequality for 3D database searching and its use in evaluating the treatment of conformational flexibility.

Authors:  J H Van Drie
Journal:  J Comput Aided Mol Des       Date:  1996-12       Impact factor: 3.686

10.  Synthesis and biological activities of potent peptidomimetics selective for somatostatin receptor subtype 2.

Authors:  L Yang; S C Berk; S P Rohrer; R T Mosley; L Guo; D J Underwood; B H Arison; E T Birzin; E C Hayes; S W Mitra; R M Parmar; K Cheng; T J Wu; B S Butler; F Foor; A Pasternak; Y Pan; M Silva; R M Freidinger; R G Smith; K Chapman; J M Schaeffer; A A Patchett
Journal:  Proc Natl Acad Sci U S A       Date:  1998-09-01       Impact factor: 11.205
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