Protein-Protein Docking with FDock 2.0 and GB-rerank Supplement
نویسندگان
چکیده
1 Details on Affinity Function Computations 2 1.1 Shape Complementarity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 1.1.1 Skin-core Definition and Weighting . . . . . . . . . . . . . . . . . . . . . . . . 2 1.1.2 FFT based formulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 1.2 Electrostatics (E). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1.2.1 FFT based formulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1.3 Interface Propensity (IP) and Hydrophobicity (HP). . . . . . . . . . . . . . . . . . . 6 1.3.1 FFT based formulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
منابع مشابه
Protein-Protein Docking with F2Dock 2.0 and GB-Rerank
MOTIVATION Computational simulation of protein-protein docking can expedite the process of molecular modeling and drug discovery. This paper reports on our new F(2) Dock protocol which improves the state of the art in initial stage rigid body exhaustive docking search, scoring and ranking by introducing improvements in the shape-complementarity and electrostatics affinity functions, a new knowl...
متن کاملImmunization with cytomegalovirus gB protein produced by the Baculovirus Expression Vector System to elicit humoral immune response in BALB/c mice
Introduction: Due to the role of neutralizing antibodies which can prevent human cytomegalovirus (HCMV) infection, most of the efforts have been focused on designing vaccines capable of eliciting protective humoral immunity. The aim of this study was to evaluate the antibody response of BALB/c mice to a truncated HCMV glycoprotein B produced in insect cells using Baculovirus Expression Vector ...
متن کاملIdentification of Agents with Potential Leishmania Malate Dehydrogenase Inhibitor Activity: A Proteomic and Molecular Docking Approach
Background and purpose: Leishmaniasis is one of the most important infectious diseases caused by different species of the Leishmania, which is a public health problem worldwide. So far, no effective vaccine is introduced for this disease and drug therapy is associated with many side effects. Therefore, this study was designed to identify novel FDA-approved compounds with anti-leishmanial activ...
متن کاملStudy of Human Albumin Protein Interaction with Fluorouracil Anticancer Drug Using Molecular Docking Method
Introduction: Drugs are mainly delivered to the target tissues by plasma proteins, such as human serum albumin, in the human body. Practical information about the thermodynamic parameters of drugs and their stability can be obtained using simulation methods, such as molecular docking. Material & Methods: This study, investigated the molecular docking of human serum albumin with fluorouracil an...
متن کاملMolecular docking study of Papaver alkaloids to some alkaloid receptors
Background and objectives: More than 40 different alkaloids have been obtained from opium the most important of which are morphine, codeine, papaverine, noscapine and tabaine. Opioid alkaloids produce analgesia by affecting areas of the brain that have peptides with pharmacological pseudo-opioid properties. These alkaloids show important effects on some intracellular peptides l...
متن کامل