As educators, we see first-hand the impact poor air quality has on our students and their families. However, Prop 30’s solution undermines funding for public education, health care, seniors, and other essential services while forcing taxpayers to pick up the tab for large corporations. Show By bypassing the state’s general fund and the voter-approved Prop 98 education funding guarantees, Prop 30 sets a dangerous precedent for big corporations to set up their own taxpayer-funded handout. Simply put, Prop 30 is a special interest carve out by a ridesharing company to get California taxpayers to foot the bill to help Lyft pay for transitioning to the use of electric vehicles. Prop 30 sets a dangerous precedent and puts the profits of Lyft ahead of the welfare of all Californians. Vote no on funneling state income tax revenue away from schools and other essential services infrastructure to a single corporation. Vote no on Prop 30. DOCK is molecular modeling program used to identify potential binding geometries and interactions of a molecule to a target. Specifically, docking is the identification of the low-energy binding modes of a small molecule, or ligand, within the active site of a macromolecule, or receptor, whose structure is known. A compound that interacts strongly with, or binds, a receptor associated with a disease may inhibit its function and thus act as a drug. Solving the docking problem computationally requires an accurate representation of the molecular energetics as well as an efficient algorithm to search the potential binding modes. Historically, the DOCK algorithm addressed rigid body docking using a geometric matching algorithm to superimpose the ligand onto a negative image of the binding pocket. Important features that improved the algorithm's ability to find the lowest-energy binding mode, including force-field based scoring, on-the-fly optimization, an improved matching algorithm for rigid body docking and an algorithm for flexible ligand docking, have been added over the years. For more information on past versions of DOCK, click here. With the release of DOCK 6, we continue to improve the algorithm's ability to predict ligand binding poses by adding new features like force-field scoring, enhanced solvation models, reference-based scoring options, and de novo design. For more information about the current release of DOCK, click here. RETURN TO TABLE OF CONTENTS 1.2. What Can DOCK Do for You
1.3. Installation
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RETURN TO TABLE OF CONTENTS DOCK RETURN TO TABLE OF CONTENTS 2.1. Overview
2.2. History
2.3. Command-line Arguments
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RETURN TO TABLE OF CONTENTS 2.10. Internal Energy Calculation
2.11. Scoring
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2.12. Minimization
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Atom Definition Elements Element Function atom type Specifies partial or complete atom type. A partial specification is more general (i.e., "C" versus "C.3"). An asterisk (*) specifies ANY atom type. ( ) Specifies atoms that must be bonded to parent atom. [ ] Specifies atoms that must NOT be bonded to parent atom. integer Specifies the number of an atom that must be bonded. Example Definitions Example Explanation C.2 ( 2 O.co2 ) A carboxylate carbon. .3 [ 3 H ] Any sp3 hybridized atom that is not attached to three hydrogens. C. [ O . ] [ N . [ 2 O.2 ] [ 2 C. ] ] Any carbon not attached to an oxygen or a nitrogen (unless the nitrogen is a nitro or tertiary nitrogen). RETURN TO TABLE OF CONTENTS
Sample Entries
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Sample Entries
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Sample File
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Sample Entries
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Sample Entries
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Sample Entries
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RETURN TO TABLE OF CONTENTS 2.14. Parallel Processing
Accessories RETURN TO TABLE OF CONTENTS 3.1. Grid
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Distance dependence of contact score function
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Generalization of the VDW component
at at
Distance dependence of the Lennard -Jones Function Precomputing potentials on a grid
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3.4. Sphgen
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3.8. Antechamber
3.9. tLEaP
3.10. Amber Score Preparation Scripts
Molecular File Formats RETURN TO TABLE OF CONTENTS 4.1. Tripos MOL2 Format
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RETURN TO TABLE OF CONTENTS References
RETURN TO TABLE OF CONTENTS Acknowledgments
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