Journal ArticleDOI
A semiempirical free energy force field with charge-based desolvation.
TLDR
The authors describe the development and testing of a semiempirical free energy force field for use in AutoDock4 and similar grid‐based docking methods based on a comprehensive thermodynamic model that allows incorporation of intramolecular energies into the predicted free energy of binding.Abstract:
The authors describe the development and testing of a semiempirical free energy force field for use in AutoDock4 and similar grid-based docking methods. The force field is based on a comprehensive thermodynamic model that allows incorporation of intramolecular energies into the predicted free energy of binding. It also incorporates a charge-based method for evaluation of desolvation designed to use a typical set of atom types. The method has been calibrated on a set of 188 diverse protein-ligand complexes of known structure and binding energy, and tested on a set of 100 complexes of ligands with retroviral proteases. The force field shows improvement in redocking simulations over the previous AutoDock3 force field.read more
Citations
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Journal ArticleDOI
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
Garrett M. Morris,Ruth Huey,William Lindstrom,Michel F. Sanner,Richard K. Belew,David S. Goodsell,Arthur J. Olson +6 more
TL;DR: AutoDock4 incorporates limited flexibility in the receptor and its utility in analysis of covalently bound ligands is reported, using both a grid‐based docking method and a modification of the flexible sidechain technique.
Journal ArticleDOI
SwissParam: a fast force field generation tool for small organic molecules.
TL;DR: A fast force field generation tool, called SwissParam, able to generate, for arbitrary small organic molecule, topologies, and parameters based on the Merck molecular force field, but in a functional form that is compatible with the CHARMM force field is presented.
Journal ArticleDOI
Computational Methods in Drug Discovery
TL;DR: Computer-aided drug discovery/design methods have played a major role in the development of therapeutically important small molecules for over three decades and theory behind the most important methods and recent successful applications are discussed.
Journal ArticleDOI
Ligand docking and binding site analysis with PyMOL and Autodock/Vina.
Daniel Seeliger,Bert L. de Groot +1 more
TL;DR: An interface between the popular molecular graphics system PyMOL and the molecular docking suites Autodock and Vina is presented and it is demonstrated how the combination of docking and visualization can aid structure-based drug design efforts.
Journal ArticleDOI
Resveratrol Ameliorates Aging-Related Metabolic Phenotypes by Inhibiting cAMP Phosphodiesterases
Sung-Jun Park,Faiyaz Ahmad,Andrew Philp,Keith Baar,Tishan Williams,Haibin Luo,Hengming Ke,Holger Rehmann,Ronald Taussig,Alexandra L. Brown,Myung K. Kim,Michael A. Beaven,Alex B. Burgin,Vincent C. Manganiello,Jay H. Chung +14 more
TL;DR: It is reported that the metabolic effects of resveratrol result from competitive inhibition of cAMP-degrading phosphodiesterases, leading to elevated cAMP levels, and administration of PDE4 inhibitors may also protect against and ameliorate the symptoms of metabolic diseases associated with aging.
References
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Journal ArticleDOI
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
Garrett M. Morris,David S. Goodsell,Robert Scott Halliday,Ruth Huey,William E. Hart,Richard K. Belew,Arthur J. Olson +6 more
TL;DR: It is shown that both the traditional and Lamarckian genetic algorithms can handle ligands with more degrees of freedom than the simulated annealing method used in earlier versions of AUTODOCK, and that the Lamarckia genetic algorithm is the most efficient, reliable, and successful of the three.
Journal ArticleDOI
A new force field for molecular mechanical simulation of nucleic acids and proteins
S. J. Weiner,Peter A. Kollman,David A. Case,U. C. Singh,Caterina Ghio,Giuliano Alagona,Salvatore Profeta,Paul K. Weiner +7 more
TL;DR: In this paper, a force field for simulation of nucleic acids and proteins is presented, which is based on the ECEPP, UNECEPP, and EPEN energy refinement software.
Journal ArticleDOI
Iterative partial equalization of orbital electronegativity – a rapid access to atomic charges
Johann Gasteiger,Mario Marsili +1 more
TL;DR: In this article, a method for the rapid calculation of atomic charges in σ-bonded and nonconjugated π-systems is presented, where only the connectivities of the atoms are considered.
Journal ArticleDOI
Docking and scoring in virtual screening for drug discovery: methods and applications.
TL;DR: Key concepts and specific features of small-molecule–protein docking methods are reviewed, selected applications are highlighted and recent advances that aim to address the acknowledged limitations of established approaches are discussed.
Journal ArticleDOI
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules.
TL;DR: The interaction of a probe group with a protein of known structure is computed at sample positions throughout and around the macromolecule, giving an array of energy values.
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