Kinetics of Processive Nucleic Acid Polymerases and Nucleases

Chou, Kuo‐Chen; Kézdy, Ferenc J.; Reusser, Fritz

doi:10.1006/abio.1994.1405

Cited by 139 publications

(80 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…One is to target the HIV (human immunodeficiency virus) reverse transcriptase (see, e.g., [165][166][167][168][169][170][171]); the other is to design HIV protease inhibitors [128,136,138,139,[172][173][174].…”

Section: Hivcleavementioning

confidence: 99%

REVIEW : Recent advances in developing web-servers for predicting protein attributes

Chou¹,

Shen²

2009

277

173

View full text Add to dashboard Cite

Recent advance in large-scale genome sequencing has generated a huge volume of protein sequences. In order to timely utilize the information hidden in these newly discovered sequences, it is highly desired to develop computational methods for efficiently identifying their various attributes because the information thus obtained will be very useful for both basic research and drug development. Particularly, it would be even more useful and welcome if a user-friendly web-server could be provided for each of these methods. In this minireview, a systematic introduction is presented to highlight the development of these web-servers by our group during the last three years.

show abstract

Section: Hivcleavementioning

confidence: 99%

REVIEW : Recent advances in developing web-servers for predicting protein attributes

Chou¹,

Shen²

2009

277

173

View full text Add to dashboard Cite

show abstract

“…Using graphic approaches to study biological systems is highly intuitive and can provide useful insights in the analysis of complicated relations in these systems, as indicated by many previous studies on a series of important biological topics, such as enzyme-catalyzed reactions (Zhou and Deng 1984;Andraos 2008;Chou 1989), proteinfolding kinetics and folding rates (Chou 1990), inhibition of HIV-1 reverse transcriptase (Althaus et al 1993), inhibition kinetics of processive nucleic acid polymerases and nucleases (Chou et al 1994), and drug metabolism systems (Chou 2010). The graphical analysis via the ''cellular automaton image'' (Wolfram 1984) has also been applied to study hepatitis B viral infections (Xiao et al 2006) and HBV virus gene missense mutation (Xiao et al 2005), as well as representing complicated biological sequences (Xiao et al 2005) and providing assistance in the identification of various important protein attributes (Xiao et al 2006(Xiao et al , 2011Xiao and Chou 2007).…”

Section: Introductionmentioning

confidence: 96%

Wavelet images and Chou’s pseudo amino acid composition for protein classification

2011

View full text Add to dashboard Cite

The last decade has seen an explosion in the collection of protein data. To actualize the potential offered by this wealth of data, it is important to develop machine systems capable of classifying and extracting features from proteins. Reliable machine systems for protein classification offer many benefits, including the promise of finding novel drugs and vaccines. In developing our system, we analyze and compare several feature extraction methods used in protein classification that are based on the calculation of texture descriptors starting from a wavelet representation of the protein. We then feed these texture-based representations of the protein into an Adaboost ensemble of neural network or a support vector machine classifier. In addition, we perform experiments that combine our feature extraction methods with a standard method that is based on the Chou's pseudo amino acid composition. Using several datasets, we show that our best approach outperforms standard methods. The Matlab code of the proposed protein descriptors is available at http://bias.csr.unibo.it/nanni/wave.rar .

show abstract

“…5,9,10,51,52 Meanwhile, various techniques in graphical approaches [55][56][57][58][59][60] as well as in computational chemistry, such as pharmacophore modeling 11 and QSAR (Quantitative StructureActivity Relationships), have been further strengthened.…”

Section: Introductionmentioning

confidence: 99%

Heuristic molecular lipophilicity potential (HMLP): A 2D‐QSAR study to LADH of molecular family pyrazole and derivatives

Mezey

Chou

2005

J Comput Chem

View full text Add to dashboard Cite

The quantum chemical and structure-based technique heuristic molecular lipophilicity potential (HMLP) is used in the liver alcohol dehydrogenase (LADH) study of molecular family pyrazole and derivatives. The molecular lipophilic index LM, molecular hydrophilic index HM, lipophilic indices lss, and hydrophilic indices hss of the substitutes (fragments), and atomic lipophilicity indices las are constructed and used in QSAR study. The HMLP indices are correlated with bioactivities of 18 pyrazole derivatives according to the 2D QSAR procedure. The multiple linear regression equation between the bioactivities of pyrazole derivatives and HMLP indices are built using partial least square (PLS) with the optimal statistical quantity (r=0.987, s=0.479, F=47.19). The inhibition mechanism of LADH of the pyrazole derivatives is explained according to the physical meaning of HMLP indices. During the HMLP calculations for the 2D QSAR, the only input parameters are the atomic van der Waals radius without the need to resort to any empirical parameters. Accordingly, HMLP can provide a rigorous theoretical approach with a crystal clear physical meaning for the 2D QSAR.

show abstract

Kinetics of Processive Nucleic Acid Polymerases and Nucleases

Cited by 139 publications

References 0 publications

REVIEW : Recent advances in developing web-servers for predicting protein attributes

REVIEW : Recent advances in developing web-servers for predicting protein attributes

Wavelet images and Chou’s pseudo amino acid composition for protein classification

Heuristic molecular lipophilicity potential (HMLP): A 2D‐QSAR study to LADH of molecular family pyrazole and derivatives

Contact Info

Product

Resources

About