run1-delwat2 (18.10.2004)

Combine analysis: run1-delwat2 (18.10.2004)

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Combine
Complex structures

1. Preparation of the pdb-files with convert.sh and xleap.sh
2. Energy minimization

restrain: protein (except H) 22, ligand (except H) 5
cycles: 200

3. Delete all waters and chloride ions, creating new cor and top files with tleap
3. Calculate Lennard-Jones and electrostatic interaction energies (anal.sh, anal.in)

PDB	alt.conf	ligand	#anal	netcharge	Ki (bovine trypsin)	deltaG (298 K) (bovine trypsin)
1o2q		A11	01	0	0.021	-43.8
1o36	195A	A02	02	-2	1.1	-34.0
1o36	195B	A02	03	-2	1.1	-34.0
1o38	195A	A03	04	+1	0.15	-39.0
1o38	195B	A03	05	+1	0.15	-39.0
1o3g		A04	06	0	0.11	-45.4
1o30		A05	07	-2	0.17	-38.6
1o2x	A08_A	A08	10	-2	1.4	-33.4
1o2x	A08_B	A08	11	-2	1.4	-33.4
1o33		A09	12	0	1.8	-32.8
1o2k		A01	14	0	0.12	-39.5

4. golpe

variables:
1-224 VDW
225-448 electrostatic
449 deltaG

PCA-scores (x axis=1, y axis=2)
(numbers are related to #anal)

PLS partial weights

variable	residue
171/395	Asp189
172/396	Ser190
174/398	Gln192
177/401	Ser195
196/420	Gly219

Prediction plot
(numbers are related to #anal)

Stereo figures of selected residues (pdf)

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