Literature DB >> 21573895

SDF2XYZ2SDF: how to exploit TINKER power in cheminformatics projects.

Paolo Tosco1, Thomas Balle, Fereshteh Shiri.   

Abstract

An open-source tool capable of converting SD files (and virtually any other format through OpenBabel) into MMFF-typed XYZ coordinate files to be used with TINKER is described. SDF2XYZ2SDF allows including the power of TINKER molecular mechanics computations in automated cheminformatics workflows, such as conformational searches and virtual screening protocols.

Mesh：

Year:  2011        PMID： 21573895     DOI： 10.1007/s00894-011-1111-7

Source DB:  PubMed          Journal:  J Mol Model        ISSN： 0948-5023            Impact factor:   1.810


  3 in total

1.  Assessing the performance of OMEGA with respect to retrieving bioactive conformations.

Authors:  Jonas Boström; Jeremy R Greenwood; Johan Gottfries
Journal:  J Mol Graph Model       Date:  2003-03       Impact factor: 2.518

2.  Ligand Entropy in Gas-Phase, Upon Solvation and Protein Complexation. Fast Estimation with Quasi-Newton Hessian.

Authors:  S Wlodek; A G Skillman; A Nicholls
Journal:  J Chem Theory Comput       Date:  2010-07-13       Impact factor: 6.006

3.  Open3DALIGN: an open-source software aimed at unsupervised ligand alignment.

Authors:  Paolo Tosco; Thomas Balle; Fereshteh Shiri
Journal:  J Comput Aided Mol Des       Date:  2011-07-27       Impact factor: 3.686
  3 in total
  2 in total

Review 1.  Open source molecular modeling.

Authors:  Somayeh Pirhadi; Jocelyn Sunseri; David Ryan Koes
Journal:  J Mol Graph Model       Date:  2016-07-30       Impact factor: 2.518

2.  Open3DALIGN: an open-source software aimed at unsupervised ligand alignment.

Authors:  Paolo Tosco; Thomas Balle; Fereshteh Shiri
Journal:  J Comput Aided Mol Des       Date:  2011-07-27       Impact factor: 3.686
  2 in total

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