Anderson Coser Gaudio | PubMed Health

PubMed2005

MoCalc: a new graphical user interface for molecular calculations.

A new computer program called MoCalc (Molecular Calculations) has been designed to help the computational chemistry practitioner in the task of performing and analyzing molecular calculations. MoCalc is a graphical user interface for the MO calculation programs Gamess and Mopac, and uses Rasmol and Babel for molecule display and file conversion, respectively. In its initial version, MoCalc can execute the following operations: (a) create and handle Gamess and Mopac input files; (b) import any kind of molecular geometry supported by Babel and paste it as Cartesian, internal, or Gaussian-type coordinates on the input file; (c) convert Gamess and Mopac output files to inputs of both programs; (d) edit and validate the keywords that control the Gamess and Mopac calculation procedure; (e) display the input (Mopac) and output (Gamess and Mopac) molecular geometries; (f) run single or multiple (batch) calculations, either interactively or in background; (g) automatically open the output files as soon as the calculation finishes; (h) extract results from the output files, such as energy, charges, dipole, population analysis, wave function, bond orders, and valence analysis, and display them in spreadsheets; (i) calculate reactivity indices derived from the frontier orbital theory and the root-mean-square (rms) deviation of input and output geometries. All the results generated by MoCalc can be promptly transferred to text editors and electronic spreadsheets, which facilitate a detailed subsequent analysis and the publication of the results. MoCalc can also perform graphical and numerical comparative analysis of the some results when more than one output file is loaded. The program was coded in Visual Basic and runs in Windows 95/98/NT4/ME/2000/XP environments.

Journal Article↗

PubMed2002

HEPT derivatives as non-nucleoside inhibitors of HIV-1 reverse transcriptase: QSAR studies agree with the crystal structures.

The interest in the non-nucleoside inhibitors (NNIs) to the reverse transcriptase (RT) as anti-AIDS agents has grown in the last ten years. The compound 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine (HEPT) is the precursor of the most studied class of NNIs, from which hundreds of derivatives have been synthesized and tested. There are at least twelve QSAR studies about the HEPT derivatives as RT inhibitors. Most of the predictions derived by these studies are related to the nature of the active site near the substituents at positions N-1 and C-5, and at the C-6 phenyl ring. The validity of these models has been checked against the 3-D structure of HIV 1 RT-HEPT complexes available. Most of these predictions were confirmed at the molecular level.

Binding Sites↗

PubMedDate not supplied

Comparison between neural networks (NN) and principal component analysis (PCA): structure activity relationships of 1,4-dihydropyridine calcium channel antagonists (nifedipine analogues).

The applicability of the neural network computer package PSDD (Perceptron Simulator for Drug Design/Perceptron-type Neural Network Simulator) in structure-activity relationship (SAR) studies was investigated. A group of 1,4-dihydropyridine derivatives was used in order to compare the PSDD results with those obtained previously with PCA. Calculated atomic and molecular descriptors using the semiempirical AM1 method were mainly used. It was shown that the predictive capability demonstrated by PSDD in SAR analysis were almost equivalent to that of PCA.

Algorithms↗