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23.02.2020 We are beggining prepare test files with programs for registered users so that everyone can use our software product.


The tests will show two linear docking algorithms: Algorithm 1 and Algorithm 2 for suitable proteins. Recall that the conditions for using linear docking are proteins that have an extended binding site along the protein polypeptide chain. Thus, the binding site of two proteins should be formed by successively arranged amino acid residues, for example, dimers Nap1-Nap1, Mdm2-Mdm2, P53-p53, -P63-P63.

Proteins that do not exactly meet the specified criteria are BCL-2 family proteins: Bax, Bcl-2, Bcl-xl, Bak, and others.


Example 1

Histone Chaperone Nap1-Nap1 Protein Dimer
UniProtKB — P25293 (NAP1_YEAST)

Algorithm 1

FILE 1

70-I QDRLGSLVGQ DSGYVGGLPK NVKEKLLSLK-100

FILE 2

70-I QDRLGSLVGQ DSGYVGGLPK NVKEKLLSLK 
TLQSELFEVE KEFQVEMFEL ENKFLQKYKP IWEQRSRIIS GQEQPKPEQI 
AKGQEIVESL NETELLVDEE EKAQNDSEEE QVKGIPSFWL TALENLPIVC 
DTITDRDAEV LEYLQDIGLE YLTDGRPGFK LLFRFDSSAN PFFTNDILCK 
TYFYQKELGY SGDFIYDHAE GCEISWKDNA HNVTVDLEMR KQRNKTTKQV 
RTIEKITPIE SFFNFFDPPK IQNEDQDEEL EEDLEERLAL DYSIGEQLKD

Algorithm 2

FILE 1

70-I QDRLGSLVGQ DSGYVGGLPK NVKEKLLSLK 
TLQSELFEVE KEFQVEMFEL ENKFLQKYKP IWEQRSRIIS GQEQPKPEQI
AKGQEIVESL NETELLVDEE EKAQNDSEEE QVKGIPSFWL TALENLPIVC
DTITDRDAEV LEYLQDIGLE YLTDGRPGFK LLFRFDSSAN PFFTNDILCK
TYFYQKELGY SGDFIYDHAE GCEISWKDNA HNVTVDLEMR KQRNKTTKQV
RTIEKITPIE SFFNFFDPPK IQNEDQDEEL EEDLEERLAL DYSIGEQLKD

FILE 2

70-I QDRLGSLVGQ DSGYVGGLPK NVKEKLLSLK 
TLQSELFEVE KEFQVEMFEL ENKFLQKYKP IWEQRSRIIS GQEQPKPEQI
AKGQEIVESL NETELLVDEE EKAQNDSEEE QVKGIPSFWL TALENLPIVC
DTITDRDAEV LEYLQDIGLE YLTDGRPGFK LLFRFDSSAN PFFTNDILCK
TYFYQKELGY SGDFIYDHAE GCEISWKDNA HNVTVDLEMR KQRNKTTKQV
RTIEKITPIE SFFNFFDPPK IQNEDQDEEL EEDLEERLAL DYSIGEQLKD

Example 2

Dimer biological complex Mdm2-Mdm2. Mouse double minute 2 homolog (MDM2) also known as E3 ubiquitin-protein ligase Mdm2 is a protein that in humans is encoded by the MDM2 gene.

UniProtKB — Q00987 (MDM2_HUMAN)

Algorithm 1

Fike 1

MCNTNMSVPTDGAVTTSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTM
KEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIY
TMIYRNLVVVNQQESSDSGTSVSENRCHLEGGSDQKDLVQELQEEKPSSS
HLVSRPSTSSRRRAISETEENSDELSGERQRKRHKSDSISLSFDESLALC
VIREICCERSSSSESTGTPSNPDLDAGVSEHSGDWLDQDSVSDQFSVEFE
VESLDSEDYSLSEEGQELSDEDDEVYQVTVYQAGESDTDSFEEDPEISLA
DYWKCTSCNEMNPPLPSHCNRCWALRENWLPEDKGKDKGEISEKAKLENS
TQAEEGFDVPDCKKTIVNDSRESCVEENDDKITQASQSQESEDYSQPSTS
SSIIYSSQEDVKEFEREETQDKEESVESSLPLNAIEPCVICQGRPKNGCI
VHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQMIVLTYFP

File 2

440-ICQGRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQ-490

Algorithm 2

File 1

MCNTNMSVPTDGAVTTSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTM
KEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIY
TMIYRNLVVVNQQESSDSGTSVSENRCHLEGGSDQKDLVQELQEEKPSSS
HLVSRPSTSSRRRAISETEENSDELSGERQRKRHKSDSISLSFDESLALC
VIREICCERSSSSESTGTPSNPDLDAGVSEHSGDWLDQDSVSDQFSVEFE
VESLDSEDYSLSEEGQELSDEDDEVYQVTVYQAGESDTDSFEEDPEISLA
DYWKCTSCNEMNPPLPSHCNRCWALRENWLPEDKGKDKGEISEKAKLENS
TQAEEGFDVPDCKKTIVNDSRESCVEENDDKITQASQSQESEDYSQPSTS
SSIIYSSQEDVKEFEREETQDKEESVESSLPLNAIEPCVICQGRPKNGCI
VHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQMIVLTYFP

File 2

MCNTNMSVPTDGAVTTSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTM
KEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIY
TMIYRNLVVVNQQESSDSGTSVSENRCHLEGGSDQKDLVQELQEEKPSSS
HLVSRPSTSSRRRAISETEENSDELSGERQRKRHKSDSISLSFDESLALC
VIREICCERSSSSESTGTPSNPDLDAGVSEHSGDWLDQDSVSDQFSVEFE
VESLDSEDYSLSEEGQELSDEDDEVYQVTVYQAGESDTDSFEEDPEISLA
DYWKCTSCNEMNPPLPSHCNRCWALRENWLPEDKGKDKGEISEKAKLENS
TQAEEGFDVPDCKKTIVNDSRESCVEENDDKITQASQSQESEDYSQPSTS
SSIIYSSQEDVKEFEREETQDKEESVESSLPLNAIEPCVICQGRPKNGCI
VHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQMIVLTYFP

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