QuBiLS-MAS, open source multi-platform software for atom- and bond-based topological (2D) and chiral (2.5D) algebraic molecular descriptors computations

Journal of Cheminformatics
José R Valdes-MartiníCarlos A Morell

Abstract

In previous reports, Marrero-Ponce et al. proposed algebraic formalisms for characterizing topological (2D) and chiral (2.5D) molecular features through atom- and bond-based ToMoCoMD-CARDD (acronym for Topological Molecular Computational Design-Computer Aided Rational Drug Design) molecular descriptors. These MDs codify molecular information based on the bilinear, quadratic and linear algebraic forms and the graph-theoretical electronic-density and edge-adjacency matrices in order to consider atom- and bond-based relations, respectively. These MDs have been successfully applied in the screening of chemical compounds of different therapeutic applications ranging from antimalarials, antibacterials, tyrosinase inhibitors and so on. To compute these MDs, a computational program with the same name was initially developed. However, this in house software barely offered the functionalities required in contemporary molecular modeling tasks, in addition to the inherent limitations that made its usability impractical. Therefore, the present manuscript introduces the QuBiLS-MAS (acronym for Quadratic, Bilinear and N-Linear mapS based on graph-theoretic electronic-density Matrices and Atomic weightingS) software designed to compute topolog...Continue Reading

References

Feb 19, 1993·Journal of Medicinal Chemistry·A C GoodW G Richards
May 24, 1996·Journal of Medicinal Chemistry·B D Silverman, D E Platt
Dec 1, 1996·Journal of Computer-aided Molecular Design·G E KelloggL H Hall
May 1, 1997·Journal of Chemical Information and Computer Sciences·J Polański
Jan 8, 1999·Journal of Computer-aided Molecular Design·C de GregorioL H Hall
Jul 13, 2000·Computers & Chemistry·J Polanski, B Walczak
Aug 14, 2001·Journal of Chemical Information and Computer Sciences·L AmatR Ponec
Oct 18, 2001·Journal of Chemical Information and Computer Sciences·H H Maw, L H Hall
Jan 5, 2002·Journal of Molecular Graphics & Modelling·E Estrada, E Molina
Jun 28, 2002·Journal of Chemical Information and Computer Sciences·Kari TuppurainenMikael Peräkylä
Jun 28, 2002·Journal of Chemical Information and Computer Sciences·Shu-Shen LiuLian-Sheng Wang
Oct 16, 2002·Journal of Chemical Information and Computer Sciences·Richard D BegerJackson O Lay
Nov 25, 2003·Journal of Chemical Information and Computer Sciences·Jaroslaw Polanski, Andrzej Bak
May 26, 2004·Bioorganic & Medicinal Chemistry·Kakali DeKunal Roy
Jul 27, 2004·Journal of Chemical Information and Computer Sciences·Richard D BegerQian Xie
Apr 6, 2005·Journal of Chemical Information and Modeling·Kejun LiuS Stanley Young
Aug 24, 2005·Bioorganic & Medicinal Chemistry·Alina Montero-TorresAlfredo Meneses-Marcel
Nov 9, 2005·Bioorganic & Medicinal Chemistry Letters·Gerardo M Casañola-MartínFrancisco Torrens
Jun 27, 2006·Current Pharmaceutical Design·Christoph SteinbeckEgon L Willighagen
Aug 1, 2006·Bioorganic & Medicinal Chemistry·Yovani Marrero-PonceYsaias J Alvarado
Nov 18, 2006·Journal of Molecular Graphics & Modelling·Juan A Castillo-GaritRichard Rotondo
Nov 17, 2007·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Yovani Marrero PonceEduardo A Castro
Jan 2, 2008·Journal of Chemical Information and Modeling·Ray M MarínEdgar E Daza
May 13, 2008·Journal of Computational Chemistry·Juan A Castillo-GaritVicente Romero-Zaldivar
May 28, 2008·Journal of Chemical Information and Modeling·John Manchester, Ryszard Czermiński
Jun 21, 2008·Journal of Chemical Information and Modeling·Huixiao HongWeida Tong
Jun 25, 2010·Journal of Chemical Information and Modeling·Denis FourchesAlexander Tropsha
Mar 23, 2011·Journal of Computational Chemistry·Chun Wei Yap

❮ Previous
Next ❯

Citations

Mar 29, 2018·Future Medicinal Chemistry·Alfredo Meneses-MarcelVicente J Arán-Redó
Dec 1, 2018·Current Topics in Medicinal Chemistry·Hai Pham-TheGerardo M Casañola-Martin
Jan 17, 2020·Molecular Informatics·Alla P ToropovaAndrey A Toropov
Nov 14, 2018·Molecular Diversity·Alejandro Speck-Planche, Marcus T Scotti
Oct 30, 2019·Molecular Diversity·Yoan Martínez-LópezF Javier Torres
Sep 25, 2020·SAR and QSAR in Environmental Research·V V KleandrovaA Speck-Planche
Nov 2, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Amit Kumar HalderMaria Natália Dias Soeiro Cordeiro
Dec 23, 2019·Environmental Science and Pollution Research International·Laura M SaavedraPablo R Duchowicz
Jun 10, 2020·Current Topics in Medicinal Chemistry·Valeria V Kleandrova, Alejandro Speck-Planche
Mar 7, 2021·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Sebastián A CuestaEdgar A Márquez
Apr 17, 2021·Journal of Cheminformatics·Amit Kumar Halder, M Natália Dias Soeiro Cordeiro
Apr 20, 2021·SAR and QSAR in Environmental Research·P R DuchowiczN C Comelli
May 1, 2021·International Journal of Molecular Sciences·Roman SzucsJasna Hradski
Jun 24, 2021·Molecular Diversity·Manish Kumar TripathiPunit Kaur
Jul 31, 2021·The Science of the Total Environment·Laura M Saavedra, Pablo R Duchowicz
Aug 28, 2021·Antibiotics·Valeria V KleandrovaAlejandro Speck-Planche
Oct 31, 2019·Journal of Chemical Information and Modeling·Ernesto Contreras-TorresJuan Carlos Sánchez-Rodríguez
Sep 3, 2021·Computational and Structural Biotechnology Journal·Paula Carracedo-ReboredoCarlos Fernandez-Lozano
Dec 11, 2021·International Journal of Molecular Sciences·Viviana Quevedo-TumailliHumberto González-Díaz

❮ Previous
Next ❯

Methods Mentioned

BETA
PCA

Software Mentioned

CODESSA
GT
Weka ARFF
Macromodel
DIVATI
mathop
Mac
DRAGON
Java JRE
HyperChem

Related Concepts

Related Feeds

Antimalarial Agents (ASM)

Antimalarial agents, also known as antimalarials, are designed to prevent or cure malaria. Discover the latest research on antimalarial agents here.

Antimalarial Agents

Antimalarial agents, also known as antimalarials, are designed to prevent or cure malaria. Discover the latest research on antimalarial agents here.