Releases · Fraternalilab/POPSlegacy

04 Nov 13:40

jkleinj

v2.3.0

43ee251

XML and compressed input; JSON output Latest

Latest

Input

This release has added capability to read XML files in plain and compressed files,
classical PDB and XML files. Decompression is performed by the ZLIB library for PDB
files and natively included in the XML library. Both libraries (zlib and libxml-2.0) are now
a mandatory dependency that is checked by 'configure'.

Output

Output can be speficied to be in JSON format. That format is compatible with the FunPDBe schema.

Assets 2

12 Jun 23:14

jkleinj

v1.8.0

b7f2216

interface: nearest neighbour atom pairlist between chains

Information of interface residues in complexes can be obtained with switch
--interfaceOut, yielding the output file 'interface.out',
For each atom of the input structure, the nearest neighbour
is computed based on the neighbour list and printed if the two contact
atoms are in different chains. Note that this pairlist is not symmetric:
atom distance A-B might be shortest for A, but distance B-C might be shortest
for B. Also, the list might change with protein motion. Therefore it depends
on the interpretation to be derived from the interface whether it is suitable
to use the atom pairs, the residue pairs and/or their distances.

Excerpt of output for '1f3r.pdb':
1 N TRP A 67 3570 O ASN B 231 3.0156
7 CD1 TRP A 67 1069 OG SER B 61 3.3179
9 NE1 TRP A 67 1069 OG SER B 61 2.8603
30 CB ASN A 68 992 CE1 TYR B 56 3.6573
32 OD1 ASN A 68 1029 N TYR B 59 3.1650
33 ND2 ASN A 68 1112 NZ LYS B 64 3.3937
43 O PRO A 69 990 CD1 TYR B 56 3.1214
....

The first 5 columns are descriptors of atom 'i', the second 5 columns are descriptors of atom 'j',
the last column is the distance between 'i' and 'j'.

Assets 2

04 Jun 23:34

jkleinj

v1.7.0

4c9dec4

bSASA output

To enable computation of 3D profiles, the buried SASA is now computed and
printed to 'popsb.out'. The buried SASA are the SASA components that are
subtracted from the isolated atom surface to arrive at the POPS* values.
These components are split into a hydrophilic and hydrophobic part,
depending on the nature on the contact (overlap) neighbour atom.
bSASA values are computed only for inter-residue contacts and for side-chain atoms,
but the contacting atom can be in the backbone.

Assets 2