Literature DB >> 20383726

Open3DQSAR: a new open-source software aimed at high-throughput chemometric analysis of molecular interaction fields.

Paolo Tosco1, Thomas Balle.   

Abstract

Open3DQSAR is a freely available open-source program aimed at chemometric analysis of molecular interaction fields. MIFs can be imported from different sources (GRID, CoMFA/CoMSIA, quantum-mechanical electrostatic potential or electron density grids) or generated by Open3DQSAR itself. Much focus has been put on automation through the implementation of a scriptable interface, as well as on high computational performance achieved by algorithm parallelization. Flexibility and interoperability with existing molecular modeling software make Open3DQSAR a powerful tool in pharmacophore assessment and ligand-based drug design.

Mesh:

Year:  2010        PMID: 20383726     DOI: 10.1007/s00894-010-0684-x

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


  9 in total

1.  Molden: a pre- and post-processing program for molecular and electronic structures.

Authors:  G Schaftenaar; J H Noordik
Journal:  J Comput Aided Mol Des       Date:  2000-02       Impact factor: 3.686

2.  GRID/CPCA: a new computational tool to design selective ligands.

Authors:  M A Kastenholz; M Pastor; G Cruciani; E E Haaksma; T Fox
Journal:  J Med Chem       Date:  2000-08-10       Impact factor: 7.446

3.  Statistical variation in progressive scrambling.

Authors:  Robert D Clark; Peter C Fox
Journal:  J Comput Aided Mol Des       Date:  2004 Jul-Sep       Impact factor: 3.686

4.  Modeling robust QSAR. 2. iterative variable elimination schemes for CoMSA: application for modeling benzoic acid pKa values.

Authors:  Rafal Gieleciak; Jaroslaw Polanski
Journal:  J Chem Inf Model       Date:  2007 Mar-Apr       Impact factor: 4.956

5.  Toward robust QSPR models: Synergistic utilization of robust regression and variable elimination.

Authors:  Rainer Grohmann; Torsten Schindler
Journal:  J Comput Chem       Date:  2008-04-30       Impact factor: 3.376

6.  Complementary three-dimensional quantitative structure-activity relationship modeling of binding affinity and functional potency: a study on alpha4beta2 nicotinic ligands.

Authors:  Paolo Tosco; Philip K Ahring; Tino Dyhring; Dan Peters; Kasper Harpsøe; Tommy Liljefors; Thomas Balle
Journal:  J Med Chem       Date:  2009-04-23       Impact factor: 7.446

Review 7.  Molecular fields in drug discovery: getting old or reaching maturity?

Authors:  Simon Cross; Gabriele Cruciani
Journal:  Drug Discov Today       Date:  2009-01-14       Impact factor: 7.851

8.  Elimination of uninformative variables for multivariate calibration.

Authors:  V Centner; D L Massart; O E de Noord; S de Jong; B M Vandeginste; C Sterna
Journal:  Anal Chem       Date:  1996-11-01       Impact factor: 6.986

9.  Smart region definition: a new way to improve the predictive ability and interpretability of three-dimensional quantitative structure-activity relationships.

Authors:  M Pastor; G Cruciani; S Clementi
Journal:  J Med Chem       Date:  1997-05-09       Impact factor: 7.446

  9 in total
  29 in total

1.  Insights into the interaction and binding mode of a set of antifungal azoles as inhibitors of potential fungal enzyme-based targets.

Authors:  Camilo Guerrero-Perilla; Freddy A Bernal; Ericsson Coy-Barrera
Journal:  Mol Divers       Date:  2018-06-29       Impact factor: 2.943

Review 2.  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

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

4.  Autogrid-based clustering of kinases: selection of representative conformations for docking purposes.

Authors:  Giovanni Marzaro; Alessandro Ferrarese; Adriana Chilin
Journal:  Mol Divers       Date:  2014-05-29       Impact factor: 2.943

5.  KRAKENX: software for the generation of alignment-independent 3D descriptors.

Authors:  Vishwesh Venkatraman; Bjørn Kåre Alsberg
Journal:  J Mol Model       Date:  2016-03-29       Impact factor: 1.810

6.  www.3d-qsar.com: a web portal that brings 3-D QSAR to all electronic devices-the Py-CoMFA web application as tool to build models from pre-aligned datasets.

Authors:  Rino Ragno
Journal:  J Comput Aided Mol Des       Date:  2019-10-08       Impact factor: 3.686

7.  Optimal strategies for virtual screening of induced-fit and flexible target in the 2015 D3R Grand Challenge.

Authors:  Zhaofeng Ye; Matthew P Baumgartner; Bentley M Wingert; Carlos J Camacho
Journal:  J Comput Aided Mol Des       Date:  2016-08-29       Impact factor: 3.686

8.  Identification and characterization of agnuside, a natural proangiogenic small molecule.

Authors:  Piyush Pillarisetti; Kenneth A Myers
Journal:  Eur J Med Chem       Date:  2018-10-05       Impact factor: 6.514

9.  Psoralen derivatives as inhibitors of NF-κB interaction: the critical role of the furan ring.

Authors:  Giovanni Marzaro; Ilaria Lampronti; Monica Borgatti; Paolo Manzini; Roberto Gambari; Adriana Chilin
Journal:  Mol Divers       Date:  2015-04-14       Impact factor: 2.943

10.  Open Babel: An open chemical toolbox.

Authors:  Noel M O'Boyle; Michael Banck; Craig A James; Chris Morley; Tim Vandermeersch; Geoffrey R Hutchison
Journal:  J Cheminform       Date:  2011-10-07       Impact factor: 5.514

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