[HTML][HTML] Geometry of nonbonded interactions involving planar groups in proteins

P Chakrabarti, R Bhattacharyya - Progress in biophysics and molecular …, 2007 - Elsevier
Although hydrophobic interaction is the main contributing factor to the stability of the protein
fold, the specificity of the folding process depends on many directional interactions. An …

Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families

JW Torrance, GJ Bartlett, CT Porter… - Journal of molecular …, 2005 - Elsevier
Catalytic site structure is normally highly conserved between distantly related enzymes. As a
consequence, templates representing catalytic sites have the potential to succeed at …

Catalytic sites of hydrolases: structures and catalytic cycles

SD Varfolomeev, IA Gariev… - Russian Chemical …, 2005 - iopscience.iop.org
The applications of various bioinformatics methods and databases to the analysis and
classification of proteins and search for active sites of enzymes are considered. The …

PAR-3D: a server to predict protein active site residues

K Goyal, D Mohanty, SC Mande - Nucleic Acids Research, 2007 - academic.oup.com
Abstract PAR-3D (http://sunserver. cdfd. org. in: 8080/protease/PAR_3D/index. html) is a
web-based tool that exploits the fact that relative juxtaposition of active site residues is a …

The fragment transformation method to detect the protein structural motifs

CH Lu, YS Lin, YC Chen, CS Yu… - Proteins: Structure …, 2006 - Wiley Online Library
To identify functional structural motifs from protein structures of unknown function becomes
increasingly important in recent years due to the progress of the structural genomics …

Clustering of protein structural fragments reveals modular building block approach of nature

AV Tendulkar, AA Joshi, MA Sohoni… - Journal of molecular …, 2004 - Elsevier
Structures of peptide fragments drawn from a protein can potentially occupy a vast
conformational continuum. We co-ordinatize this conformational space with the help of …

Prediction of active site cleft using support vector machines

S Sonavane, P Chakrabarti - Journal of chemical information and …, 2010 - ACS Publications
Computational tools are available today for the detection and delineation of the clefts and
cavities in protein 3D structure and ranking them on the basis of probable binding site clefts …

Some operations research methods for analyzing protein sequences and structures

P Łukasiak, J Błażewicz, M Miłostan - Annals of Operations Research, 2010 - Springer
The operations research is probably one of the most successful field of applied mathematics
used in economics, physics, chemistry, almost everywhere where one has to analyze huge …

Some operations research methods for analyzing protein sequences and structures

J Błażewicz, P Łukasiak, M Miłostan - 4OR, 2006 - Springer
Operations Research is probably one of the most successful fields of applied mathematics
used in Economics, Physics, Chemistry, almost everywhere one has to analyze huge …

Substrate specificity of lipases in alkoxycarbonylation reaction: QSAR model development and experimental validation

SM Chandrasekaran, S Bhartiya… - Biotechnology and …, 2006 - Wiley Online Library
Although lipases are known to catalyze alkoxycarbonylation reactions in organic solvents,
the existing knowledge base on their substrate specificity in alkoxycarbonylation reaction is …