Literature DB >> 11606783

Conformation-family Monte Carlo: a new method for crystal structure prediction.

J Pillardy1, Y A Arnautova, C Czaplewski, K D Gibson, H A Scheraga.   

Abstract

A new global optimization method, Conformation-family Monte Carlo, has been developed recently for searching the conformational space of macromolecules. In the present paper, we adapted this method for prediction of crystal structures of organic molecules without assuming any symmetry constraints except the number of molecules in the unit cell. This method maintains a database of low energy structures that are clustered into families. The structures in this database are improved iteratively by a Metropolis-type Monte Carlo procedure together with energy minimization, in which the search is biased toward the regions of the lowest energy families. The Conformation-family Monte Carlo method is applied to a set of nine rigid and flexible organic molecules by using two popular force fields, AMBER and W99. The method performed well for the rigid molecules and reasonably well for the molecules with torsional degrees of freedom.

Mesh:

Year:  2001        PMID: 11606783      PMCID: PMC60057          DOI: 10.1073/pnas.231479298

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  3 in total

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Journal:  Acta Crystallogr B       Date:  2000-08

2.  Structure predictions allowing more than one molecule in the asymmetric unit

Authors: 
Journal:  Acta Crystallogr B       Date:  2000-06

3.  Monte Carlo-minimization approach to the multiple-minima problem in protein folding.

Authors:  Z Li; H A Scheraga
Journal:  Proc Natl Acad Sci U S A       Date:  1987-10       Impact factor: 11.205

  3 in total
  8 in total

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Journal:  Eur Biophys J       Date:  2007-03-21       Impact factor: 1.733

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Journal:  J Comput Aided Mol Des       Date:  2018-11-30       Impact factor: 3.686

4.  Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein-Ligand Docking.

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Journal:  J Chem Theory Comput       Date:  2021-02-12       Impact factor: 6.006

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Journal:  Phys Chem Chem Phys       Date:  2011-06-08       Impact factor: 3.676

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Journal:  Proteins       Date:  2011-02

7.  Towards crystal structure prediction of complex organic compounds--a report on the fifth blind test.

Authors:  David A Bardwell; Claire S Adjiman; Yelena A Arnautova; Ekaterina Bartashevich; Stephan X M Boerrigter; Doris E Braun; Aurora J Cruz-Cabeza; Graeme M Day; Raffaele G Della Valle; Gautam R Desiraju; Bouke P van Eijck; Julio C Facelli; Marta B Ferraro; Damian Grillo; Matthew Habgood; Detlef W M Hofmann; Fridolin Hofmann; K V Jovan Jose; Panagiotis G Karamertzanis; Andrei V Kazantsev; John Kendrick; Liudmila N Kuleshova; Frank J J Leusen; Andrey V Maleev; Alston J Misquitta; Sharmarke Mohamed; Richard J Needs; Marcus A Neumann; Denis Nikylov; Anita M Orendt; Rumpa Pal; Constantinos C Pantelides; Chris J Pickard; Louise S Price; Sarah L Price; Harold A Scheraga; Jacco van de Streek; Tejender S Thakur; Siddharth Tiwari; Elisabetta Venuti; Ilia K Zhitkov
Journal:  Acta Crystallogr B       Date:  2011-11-17

8.  Convergence Properties of Crystal Structure Prediction by Quasi-Random Sampling.

Authors:  David H Case; Josh E Campbell; Peter J Bygrave; Graeme M Day
Journal:  J Chem Theory Comput       Date:  2016-01-13       Impact factor: 6.006

  8 in total

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