Properties used in Pelikan - Additional Attributes and Values for Pelikan and NAOMInova 143

B. Additional Attributes and Values for Pelikan and NAOMInova 143

B.5. Properties used in Pelikan

Property name Description Value range

Element Count of each element type present in a reference ligand. The exact element types used are listed in B.2

0-100 (integer)

Functional group Count of each functional group present in a reference ligand. The exact functional groups used are listed in B.1

0-100 (integer)

MW Molecular weight 0-1·10⁹ (real)

Atoms Number of heavy atoms 0-100 (integer)

TPSA Topological polar surface ares 0-1·10⁹ (real) logP logP after Wildman and Crippen [133] -1.0-1000 (real)

Volume Volume of molecule 0-1·10⁶ (real)

Total charge Total charge of molecule

Acceptors Number of hydrogen bond acceptors in molecule

0-100 (integer) Donors Number of hydrogen bond donors in

molecule

0-100 (integer) LipinskiDonors Number of hydrogens bound to oxygen

or nitrogen

0-100 (integer)

Table B.3.: Properties calculated for reference ligands in Pelikan, part 1.

Hetero Number of hetero atoms in molecule 0-100 (integer) AromAtoms Number of aromatic atoms in molecule 0-100 (integer) Halogens Number of halogens in molecule 0-100 (integer) Inorganic Number of atoms not in organic subset 0-100 (integer) LipinskiAcceptors Number of nitrogens and oxygens 0-100 (integer) RotB Number of rotatable bonds in molecule 0-400 (integer)

CRTB Maximum path of contiguous rotatable

bonds

0-400 (integer)

Rings Number of rings 0-99 (integer)

URFs Number of unique ring families 0-99 (integer)

AroRings Number of aromatic rings 0-99 (integer)

MaxRing Biggest ring 0-100 (integer)

Ringsystems Number of ringsystems in molecule 0-99 (integer) AroRingsystems Number of aromatic ringsystems in

molecule

0-99 (integer) MaxRSsize Biggest ringsystem in molecule 0-100 (integer) RS Number of stereo centers in molecule 0-100 (integer)

EZ Number of stereo bonds in molecule 0-400 (integer)

Cyclomatic Number Cyclomatic Number of molecule 0-99 (integer) Max Cyclomatic Number Maximum Cyclomatic Number of

molecule’s ringsystems

0-99 (integer)

Table B.4.: Properties calculated for reference ligands in Pelikan, part 2.

Property name Description Value range

PFAM id id of protein in PFAM database [134] ’PF’+five digit number Uniprot id id of protein in uniprot database [135] string

EC number enzyme commission number four numbers, 0-99 (integer)

Organism organism of protein string

Table B.5.: Properties calculated for proteins in Pelikan.

Property name Description Value range Ligand name Name of reference ligand no limit of length

(string) Amino acids in pocket Count of each amino acid in the

pocket

0-100 (integer)

Volume Volume of pocket 0-5000 (real)

Surface Surface of pocket 0-5000 (real)

Surface-Volume-Ratio Ratio of surface and volume 0-5000 (real) HeavyAtoms Number of heavy atoms in pocket 0-1000 (integer) Acceptors Number of H-bond acceptors 0-100 (integer)

Donors Number of H-bond donors 0-100 (integer)

Hydrophobicity Hydrophobicity of pocket 0-1 (real)

Depth Depth of pocket 0-5000 (real)

Enclosure Enclosure 0-5000 (real)

Score Simple DogSite score 0-5000 (real)

Metal Number of metal atoms in Pocket 0-100 (integer) Table B.6.: Properties calculated for pockets in Pelikan.

Property name Description Value range

Name Content of PDB title entry no limit of length

(string)

PDB id id of PDB file no limit of length

(string)

Resolution Resolution of PDB file 0-4 (real)

Experimental source Experiment type which has been used to generate the structure of the pro-tein. The following types can be used:

Unknown, NMR solution, NMR solid state, X-ray, fiber diffraction, neutron diffraction, electron microscopy, elec-tron crystallography, solution scatter-ing

enum (integer)

Table B.7.: Properties calculated for protein-ligand complexes in Pelikan.

C

Test Queries Pelikan

OnePoint - no point-point constraints

Search point 1: Original Molecule = Reference ligand, Element = Oxygen, Interaction type = Undefined, Functional group = any, Amino acid = Any, Atom name = Any, Sec. structure = Any, Amino acid location

= Any

TwoPoints - standard

= Any

TwoPoints - no point-point constraints

= Any

TwoPoints - element and interaction type

Search point 1: Original Molecule = Reference ligand, Element = Oxygen, Interaction type = Acceptor, Functional group = any, Amino acid = Any, Atom name = Any, Sec. structure = Any, Amino acid location

= Any

Search point 2: Original Molecule = Protein, Element = Nitrogen, Interaction type = Donor, Functional group = any, Amino acid = Any, Atom name = Any, Sec. structure = Any, Amino acid location = Any Distance constraint between search points 1-2: min = 6.1 ˚A, max = 7.1 ˚A

TwoPoints - all properties

= Any

Search point 2: Original Molecule = Protein, Element = Nitrogen, Interaction type = Donor, Functional group = any, Amino acid = VAL, Atom name = N, Sec. structure = Sheet, Amino acid location = Backbone Distance constraint between search points 1-2: min = 6.1 ˚A, max = 7.1 ˚A

TwoPoints - resolution

= Any

Additional filter: Resolution between 1.5 and 2.5 ˚A

TwoPoints - resolution and pocket volume

= Any

Additional filter: Resolution between 1.5 and 2.5 ˚A, pocket volume between 650 and 750 ˚A³

TwoPoints - 3-4 ˚A

= Any

TwoPoints - 6-7 ˚A

Search point 1: Original Molecule = Reference ligand, Element = Oxygen, Interaction type = Undefined, Functional group = any, Amino acid = Any, Atom name = , Sec. structure = Any, Amino acid location = Any

Search point 2: Original Molecule = Protein, Element = Nitrogen, Interaction type = Undefined, Functional group = any, Amino acid = Any, Atom name = , Sec. structure = Any, Amino acid location = Any Distance constraint between search points 1-2: min = 6 ˚A, max = 7 ˚A

TwoPoints - 9-10 ˚A

= Any

TwoPoints - short SMARTS

= Any, SMARTS = [$(OCC)]

Distance constraint between search points 1-2: min = 6.1 ˚A, max = 7.1 ˚A

TwoPoints - short SMARTS + point attributes

= Any, SMARTS = [$(OCC)]

Distance constraint between search points 1-2: min = 6.1 ˚A, max = 7.1 ˚A

TwoPoints - long SMARTS

Search point 1: Original Molecule = Reference ligand, Element = Oxygen, Interaction type = Undefined, Functional group = Any, Amino acid = Any, Atom name = Any, Sec. structure = Any, Amino acid location

= Any, SMARTS = [$(O(CCO)POP)]

Distance constraint between search points 1-2: min = 6.1 ˚A, max = 7.1 ˚A

TwoPoints - long SMARTS + point attributes

= Any, SMARTS = [$(O(CCO)POP)]

Distance constraint between search points 1-2: min = 6.1 ˚A, max = 7.1 ˚A

ThreePoints - standard

= Any

Search point 2: Original Molecule = Protein, Element = Nitrogen, Interaction type = Undefined, Functional group = any, Amino acid = Any, Atom name = Any, Sec. structure = Any, Amino acid location = Any Search point 3: Original Molecule = Reference ligand, Element = Nitrogen, Interaction type = Undefined, Functional group = any, Amino acid = Any, Atom name = Any, Sec. structure = Any, Amino acid location

= Any

Distance constraint between search points 1-2: min = 6.1 ˚A, max = 7.1 ˚A Distance constraint between search points 2-3: min = 7.6 ˚A, max = 8.6 ˚A

ThreePoints - no point-point constraints

= Any

ThreePoints - resolution

= Any

Distance constraint between search points 1-2: min = 6.1 ˚A, max = 7.1 ˚A Distance constraint between search points 2-3: min = 7.6 ˚A, max = 8.6 ˚A Additional filter: Resolution between 1.5 and 2.5 ˚A

ThreePoints - resolution and pocket volume

= Any

Distance constraint between search points 1-2: min = 6.1 ˚A, max = 7.1 ˚A Distance constraint between search points 2-3: min = 7.6 ˚A, max = 8.6 ˚A

Additional filter: Resolution between 1.5 and 2.5 ˚A, pocket volume between 650 and 750 ˚A³

ThreePoints - 3-4 ˚A

= Any

ino acid location = Any

Distance constraint between search points 1-2: min = 3 ˚A, max = 4 ˚A

Distance constraint between search points 2-3: min = 4 ˚A, max = 5 ˚A//if set to 3-4 ˚A, no results were found

ThreePoints - 6-7 ˚A

= Any

Distance constraint between search points 1-2: min = 6 ˚A, max = 7 ˚A Distance constraint between search points 2-3: min = 6 ˚A, max = 7 ˚A

ThreePoints - 9-10 ˚A

= Any

Distance constraint between search points 1-2: min = 9 ˚A, max = 10 ˚A Distance constraint between search points 2-3: min = 9 ˚A, max = 10 ˚A

ThreePoints - short SMARTS

= Any, SMARTS = [$(OCC)]

Search point 3: Original Molecule = Reference ligand, Element = Nitrogen, Interaction type = Undefined, Functional group = any, Amino acid = Any, Atom name = Any, Sec. structure = Any, Amino acid location

= Any, SMARTS = [$(NPO)]

Distance constraint between search points 1-2: min = 6.1 ˚A, max = 7.1 ˚A Distance constraint between search points 2-3: min = 7.6 ˚A, max = 8.6 ˚A

ThreePoints - short SMARTS + point attributes

= Any, SMARTS = [$(OCC)]

Search point 2: Original Molecule = Reference ligand, Element = Nitrogen, Interaction type = Donor, Func-tional group = any, Amino acid = Any, Atom name = Any, Sec. structure = Any, Amino acid location = Any, SMARTS = [$(NPO)]

Distance constraint between search points 1-2: min = 6.1 ˚A, max = 7.1 ˚A Distance constraint between search points 2-3: min = 7.6 ˚A, max = 8.6 ˚A

ThreePoints - long SMARTS

= Any, SMARTS = [$(NC(C(C)C)C=O)]

SMARTS = [$(NC(C(C)C)C=O)]

= Any, SMARTS = [$(N(P(O)(O)=O)P(O)(O)=O)]

Distance constraint between search points 1-2: min = 6.1 ˚A, max = 7.1 ˚A Distance constraint between search points 2-3: min = 7.6 ˚A, max = 8.6 ˚A

ThreePoints - long SMARTS + point attributes

= Any, SMARTS = [$(NC(C(C)C)C=O)]

Search point 3: Original Molecule = Reference ligand, Element = Nitrogen, Interaction type = Donor, Func-tional group = any, Amino acid = Any, Atom name = Any, Sec. structure = Any, Amino acid location = Any, SMARTS = [$(N(P(O)(O)=O)P(O)(O)=O)]

Distance constraint between search points 1-2: min = 6.1 ˚A, max = 7.1 ˚A Distance constraint between search points 2-3: min = 7.6 ˚A, max = 8.6 ˚A

FourPoints - standard

= Any

Search point 4: Original Molecule = Protein, Element = Oxygen, Interaction type = Undefined, Functional group = any, Amino acid = Any, Atom name = Any, Sec. structure = Any, Amino acid location = Any Distance constraint between search points 1-2: min = 6.1 ˚A, max = 7.1 ˚A

Distance constraint between search points 2-3: min = 7.6 ˚A, max = 8.6 ˚A Distance constraint between search points 3-4: min = 4.1 ˚A, max = 5.1 ˚A

FourPoints - no point-point constraints

= Any

Search point 4: Original Molecule = Protein, Element = Oxygen, Interaction type = Undefined, Functional group = any, Amino acid = Any, Atom name = Any, Sec. structure = Any, Amino acid location = Any

FourPoints - resolution

= Any

Distance constraint between search points 2-3: min = 7.6 ˚A, max = 8.6 ˚A Distance constraint between search points 3-4: min = 4.1 ˚A, max = 5.1 ˚A Additional filter: Resolution between 1.5 and 2.5 ˚A

FourPoints - resolution and pocket volume

= Any

Distance constraint between search points 2-3: min = 7.6 ˚A, max = 8.6 ˚A Distance constraint between search points 3-4: min = 4.1 ˚A, max = 5.1 ˚A

Additional filter: Resolution between 1.5 and 2.5 ˚A, pocket volume between 650 and 750 ˚A³

FourPoints - one distance 2 ˚A

= Any

Distance constraint between search points 2-3: min = 7.6 ˚A, max = 8.6 ˚A Distance constraint between search points 3-4: min = 4.1 ˚A, max = 5.1 ˚A

FourPoints - one distance 3 ˚A

= Any

Distance constraint between search points 2-3: min = 7.6 ˚A, max = 8.6 ˚A Distance constraint between search points 3-4: min = 4.1 ˚A, max = 5.1 ˚A

FourPoints - 3-4 ˚A

= Any

Distance constraint between search points 2-3: min = 4 ˚A, max = 5 ˚A//if set to 3-4 ˚A, no results were found Distance constraint between search points 3-4: min = 3 ˚A, max = 4 ˚A

FourPoints - 6-7 ˚A

= Any

Distance constraint between search points 2-3: min = 6 ˚A, max = 7 ˚A Distance constraint between search points 3-4: min = 6 ˚A, max = 7 ˚A

FourPoints - 9-10 ˚A

= Any

Im Dokument Mining of Interaction Geometries in Collections of Protein Structures (Seite 162-200)