Test Set Construction SB2024 V1 DOCK6.10 A

!!!!!!Under Construction!!!!!!

The purpose of this tutorial is to develop a uniform method for adding systems to the Rizzo Lab test set, and rebuilding the set from initial files. This is the protocol to be used by all lab members. If the protocol is changed, a new tutorial should be made, preserving this tutorial.

I.Introduction

A key development for this tutorial is bookkeeping scripts to manage the count of heavy atoms during processing and indicate unaccounted changes. Test cases are also included which should be visually inspected for indicated elements to be sure that processing occurred as expected.

III.Test Cases for Preparation Integrity

These are cases which that need to be visually inspected to ensure key operations during preparation were executed. This step is crucial after building the test set in batch mode.

System	Element	Details
2GQG	PhosphoTyrosine Residue	Check Residue 171 correctly has Y2P phosphotyrosine (See Picture below)
2Y03	Disulfide Bond	Check bond Residue 82.SG and Residue 167.SG is actually bonded (See Picture below )
4WMZ	Heme	Check Heme is correctly incorporated, including Iron (Fe)
1P44	NADH Cofactor	Make sure cofactor is present in 1P44.rec.clean.mol2 and grid.out as residue "COF"
5UPG	Zinc Chelated Histidine Protonation	Residue should have HID protonation (See Picture below)
3D94	NonStandard Residue Defined Mutatation	Make sure Residue 146 successfully mutates to Residue "MET" from "MHO"

IV.To Do

1. Integrate prep and frcmod files for cofactors available at http://amber.manchester.ac.uk/

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

Tutorial Written By: Christopher Corbo, Rizzo Lab, Stony Brook University (2024)

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

https://github.com/rizzolab/Testset_Protocols.git