3D QSAR in Drug Design: Ligand-Protein Interactions and by Hugo Kubinyi, Gerd Folkers, Yvonne C. Martin

By Hugo Kubinyi, Gerd Folkers, Yvonne C. Martin

Volumes 2 and three of the 3D QSAR in Drug layout sequence target to check the growth being made in CoMFA and different 3D QSAR methods because the booklet of the hugely winning first quantity approximately 4 years in the past. quantity 2 (Ligand-Protein Interactions and Molecular Similarity) divides into 3 sections facing Ligand-Protein Interactions, Quantum Chemical versions and Molecular Dynamics Simulations, and Pharmacophore Modelling and Molecular Similarity, respectively. quantity three (Recent Advances) can also be divided into 3 sections, specifically 3D QSAR technique: CoMFA and comparable methods, Receptor versions and different 3D QSAR techniques, and 3D QSAR functions. greater than seventy unusual scientists have contributed approximately 40 stories in their paintings and comparable learn to those volumes that are of remarkable caliber and timeliness. those works current an up to date assurance of the most recent advancements in all fields of 3D QSAR.

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Extra resources for 3D QSAR in Drug Design: Ligand-Protein Interactions and Molecular Similarity, Vol. 2

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For these ligand–protein complexes. molecular surfaces have been generated using the Connolly algorithm [62] and Bondi vdW radii [63]. The interface surface area for each atom was then catalogued. using a packing score. 8 Å: (7) where dab is the distance between surface elements a and b, and θ(ra, rb) is the angle formed by the surface normal vectors ra and rb at these points. For each surface element. the area was totaled for each atom pair and used to determine the atom–atom preference score, Pij, as the ratio of the total interfacial area contributed by each atom pair.

2) can also be written as: (3) where is separated at equilibrium into solvation effects (∆ Gsol), and two components for the process in vacuum: the internal energy (∆ Uvac) and entropy (T∆ Svac). ∆ Gsol can be calculated with a variety of methods [58], while T∆ Svac is often related to the number of non-methyl single bonds [47]. Both ∆Gsol and T∆Svac are assumed to have similar values for congeneric series, hence Eq. 3 is widely used in QSAR studies by expanding only the internal energy term: (4) which includes the steric (vdW ) and electrostatic (coul) aspects of the ligand-receptor interaction ( and ), the distortions (distort) induced by this interaction in both ligand and receptor ( and ) and the ligand-induced conformational changes of the receptor ( reprsents agonist-induced conformational rearrangements of the receptor that may be an important component of signal transduction and are not considered to occur upon antagonist binding to the same receptor [60].

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