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318
RESEARCH ARTICLE Study of the Differential Activity of Thrombin Inhibitors Using Docking, QSAR, Molecular Dynamics, and MM-GBSA
"... Non-peptidic thrombin inhibitors (TIs; 177 compounds) with diverse groups at motifs P1 (such as oxyguanidine, amidinohydrazone, amidine, amidinopiperidine), P2 (such as cyano-fluorophenylacetamide, 2-(2-chloro-6-fluorophenyl)acetamide), and P3 (such as pheny-lethyl, arylsulfonate groups) were studie ..."
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studied using molecular modeling to analyze their interactions with S1, S2, and S3 subsites of the thrombin binding site. Firstly, a protocol com-bining docking and three dimensional quantitative structure–activity relationship was per-formed. We described the orientations and preferred active
Structure-Based Drug Design: Docking and Scoring
"... Abstract: This review gives an introduction into ligand – receptor docking and illustrates the basic underlying concepts. An overview of different approaches and algorithms is provided. Although the application of docking and scoring has led to some remarkable successes, there are still some major c ..."
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Cited by 6 (0 self)
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Abstract: This review gives an introduction into ligand – receptor docking and illustrates the basic underlying concepts. An overview of different approaches and algorithms is provided. Although the application of docking and scoring has led to some remarkable successes, there are still some major
Receptor-Based Computational Screening of Compound Databases: The Main Docking-Scoring Engines
"... Abstract: The processes used by academic and industrial scientists to discover new drugs have recently experienced a true renaissance with many new and exciting techniques. The number of protein structures and/or chemical ligands is constantly growing, through the use of parallel chemistry, X-ray cr ..."
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Cited by 3 (0 self)
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Abstract: The processes used by academic and industrial scientists to discover new drugs have recently experienced a true renaissance with many new and exciting techniques. The number of protein structures and/or chemical ligands is constantly growing, through the use of parallel chemistry, X
A model binding site for testing scoring functions in molecular docking
- J. Mol. Biol
"... Prediction of interaction energies between ligands and their receptors remains a major challenge for structure-based inhibitor discovery. Much effort has been devoted to developing scoring schemes that can success-fully rank the affinities of a diverse set of possible ligands to a binding site for w ..."
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Cited by 20 (10 self)
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Prediction of interaction energies between ligands and their receptors remains a major challenge for structure-based inhibitor discovery. Much effort has been devoted to developing scoring schemes that can success-fully rank the affinities of a diverse set of possible ligands to a binding site
Predicting the Functions and Specificity of Triterpenoid Synthases: A Mechanism-Based Multi-intermediate Docking Approach
, 2014
"... Terpenoid synthases construct the carbon skeletons of tens of thousands of natural products. To predict functions and specificity of triterpenoid synthases, a mechanism-based, multi-intermediate docking approach is proposed. In addition to enzyme function prediction, other potential applications of ..."
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Terpenoid synthases construct the carbon skeletons of tens of thousands of natural products. To predict functions and specificity of triterpenoid synthases, a mechanism-based, multi-intermediate docking approach is proposed. In addition to enzyme function prediction, other potential applications
Adverse Drug Reaction Prediction Using Scores Produced by Large-Scale Drug-Protein Target Docking on High-Performance Computing Machines
"... Late-stage or post-market identification of adverse drug reactions (ADRs) is a significant public health issue and a source of major economic liability for drug development. Thus, reliable in silico screening of drug candidates for possible ADRs would be advantageous. In this work, we introduce a co ..."
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computational approach that predicts ADRs by combining the results of molecular docking and leverages known ADR information from DrugBank and SIDER. We employed a recently parallelized version of AutoDock Vina (VinaLC) to dock 906 small molecule drugs to a virtual panel of 409 DrugBank protein targets. L1
Docking: Successes and Challenges
"... Abstract: The state of the art of various computational aspects of docking-based virtual screening of database of small molecules is presented. The review encompasses the different search algorithms and the scoring functions used in docking methods and their applications to protein and nucleic acid ..."
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Cited by 5 (0 self)
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Abstract: The state of the art of various computational aspects of docking-based virtual screening of database of small molecules is presented. The review encompasses the different search algorithms and the scoring functions used in docking methods and their applications to protein and nucleic acid
Protein-Ligand Interactions: Docking, Design and Protein Conformational Change Thesis by
, 2002
"... Virtual ligand screening has proven to be a successful strategy in drug design. An in house-developed procedure (HierDock), a coarse grain docking method followed by a fine grain search procedure, was used to determine the binding site for sugars in the outer membrane protein A in E.coli, a key inte ..."
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understanding of binding mechanism in aminoacyl tRNA synthetases by attempting to design these enzymes to bind to non-natural amino acids. Using the computational protein design software (ORBIT), a phenylalanyl-tRNA synthetase variant that allows
Designing of Protein Kinase C β-II Inhibitors against Diabetic complications: Structure Based Drug Design, Induced Fit docking and analysis of active site conformational changes
, 2012
"... Protein Kinase C β-II (PKC β-II) is an important enzyme in the development of diabetic complications like cardiomyopathy, retinopathy, neuropathy, nephropathy and angiopathy. PKC β-II is activated in vascular tissues during diabetic vascular abnormalities. Thus, PKC β-II is considered as a potent dr ..."
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complexes showed favorable docking score, glide energy, glide emodel and hydrogen bond and hydrophobic interactions with the active site of PKC β-II. Binding free energy was calculated for IFD complexes using Prime MM-GBSA method. The conformational changes induced by the inhibitor at the active site of PKC
Results 1 - 10
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318
