Literature DB >> 10721501

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

G Schaftenaar1, J H Noordik.   

Abstract

Molden is a software package for pre- and postprocessing of computational chemistry program data. Interfacing to the ab initio programs Games-US/UK and Gaussian and to the semi-empirical package MOPAC is provided. The emphasis is on computation and visualization of electronic and molecular properties but, e.g., reaction pathways can be simulated as well. Some molecular properties of interest are processed directly from the output of the computational chemistry programs, others are calculated in MOLDEN before display. The package features different options to display MOLecular electronic DENsity, each focusing on a different structural aspect: molecular orbitals, electron density, molecular minus atomic density and the Laplacian of the electron density. To display difference density, either the spherically averaged atomic density or the oriented ground state atomic density can be used for a number of standard basis sets. The quantum mechanical electrostatic potential or a distributed multiple expansion derived electrostatic potential can be calculated and atomic charges can be fitted to these potentials calculated on Connolly surface(s). Reaction pathways and molecular vibrations can be visualized. Input structures can be generated with a Z-matrix editor. A variety of graphics languages is supported: XWindows, postscript, VRML and Povray format.

Mesh:

Year:  2000        PMID: 10721501     DOI: 10.1023/a:1008193805436

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


  1 in total

1.  The Protein Data Bank: a computer-based archival file for macromolecular structures.

Authors:  F C Bernstein; T F Koetzle; G J Williams; E F Meyer; M D Brice; J R Rodgers; O Kennard; T Shimanouchi; M Tasumi
Journal:  J Mol Biol       Date:  1977-05-25       Impact factor: 5.469

  1 in total
  194 in total

1.  The effect of isodensity surface sampling on ESP derived charges and the effect of adding bondcenters on DMA derived charges.

Authors:  G Schaftenaar; J H Noordik
Journal:  J Comput Aided Mol Des       Date:  2000-03       Impact factor: 3.686

2.  Peptide-plane flipping in proteins.

Authors:  S Hayward
Journal:  Protein Sci       Date:  2001-11       Impact factor: 6.725

3.  Deletion of a single hydrogen bonding atom from the MS2 RNA operator leads to dramatic rearrangements at the RNA-coat protein interface.

Authors:  E Grahn; N J Stonehouse; C J Adams; K Fridborg; L Beigelman; J Matulic-Adamic; S L Warriner; P G Stockley; L Liljas
Journal:  Nucleic Acids Res       Date:  2000-12-01       Impact factor: 16.971

4.  The perspectives of computational chemistry modeling.

Authors:  Igor V Tetko
Journal:  J Comput Aided Mol Des       Date:  2011-12-11       Impact factor: 3.686

5.  Thermodynamic coupling of protonation and conformational equilibria in proteins: theory and simulation.

Authors:  Chuanyin Shi; Jason A Wallace; Jana K Shen
Journal:  Biophys J       Date:  2012-04-03       Impact factor: 4.033

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Authors:  Paolo Tosco; Thomas Balle
Journal:  J Mol Model       Date:  2010-04-11       Impact factor: 1.810

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Authors:  Leonel E Rojo; Jans Alzate-Morales; Iván N Saavedra; Peter Davies; Ricardo B Maccioni
Journal:  J Alzheimers Dis       Date:  2010       Impact factor: 4.472

8.  Surface residues dynamically organize water bridges to enhance electron transfer between proteins.

Authors:  Aurélien de la Lande; Nathan S Babcock; Jan Rezác; Barry C Sanders; Dennis R Salahub
Journal:  Proc Natl Acad Sci U S A       Date:  2010-06-14       Impact factor: 11.205

9.  Integrating molecular docking, DFT and CoMFA/CoMSIA approaches for a series of naphthoquinone fused cyclic α-aminophosphonates that act as novel topoisomerase II inhibitors.

Authors:  Yi Ma; Jian-Guo Wang; Bin Wang; Zheng-Ming Li
Journal:  J Mol Model       Date:  2010-11-25       Impact factor: 1.810

10.  Molecular dynamics simulation of transmembrane polypeptide orientational fluctuations.

Authors:  David J Goodyear; Simon Sharpe; Chris W M Grant; Michael R Morrow
Journal:  Biophys J       Date:  2004-10-15       Impact factor: 4.033

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