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Figure 3 | BMC Bioinformatics

Figure 3

From: Structural descriptor database: a new tool for sequence-based functional site prediction

Figure 3

Creating HMM descriptors from SCOP families. Each SCOP family was segmented in structural groups and HMM descriptors were created from these groups. A – Image shows the building of HMM descriptors for a hypothetical family, namely f1. First, A f 1 MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaemyqae0aaSbaaSqaaiabdAgaMnaaBaaameaacqaIXaqmaeqaaaWcbeaaaaa@2F89@ is built by aligning all proteins of S G f 1 MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaem4uamLaem4raC0aaSbaaSqaaiabdAgaMnaaBaaameaacqaIXaqmaeqaaaWcbeaaaaa@30C4@ structural group. Next, HMM f 1 MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaeeisaGKaeeyta0Kaeeyta00aaSbaaSqaaiabdAgaMnaaBaaameaacqaIXaqmaeqaaaWcbeaaaaa@31D7@ is built from both A f 1 MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaemyqae0aaSbaaSqaaiabdAgaMnaaBaaameaacqaIXaqmaeqaaaWcbeaaaaa@2F89@ alignment and functional site positions of A f 1 MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaemyqae0aaSbaaSqaaiabdAgaMnaaBaaameaacqaIXaqmaeqaaaWcbeaaaaa@2F89@ , called B f 1 MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaemOqai0aaSbaaSqaaiabdAgaMnaaBaaameaacqaIXaqmaeqaaaWcbeaaaaa@2F8B@ . Finally, f1 is divided into groups of proteins that interact with the same ligand, and HMM f 1 L i MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaeeisaGKaeeyta0Kaeeyta00aaSbaaSqaaiabdAgaMnaaBaaameaacqaIXaqmaeqaaaWcbeaakiabdYeamnaaBaaaleaacqWGPbqAaeqaaaaa@3489@ are built in the same way, since L is the number of ligand and 1 ≤ iN. B – In order, for building HMM classifications, the consensus-sequence f 1 MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaee4yamMaee4Ba8MaeeOBa4Maee4CamNaeeyzauMaeeOBa4Maee4CamNaeeyDauNaee4CamNaeeyla0Iaee4CamNaeeyzauMaeeyCaeNaeeyDauNaeeyzauMaeeOBa4Maee4yamMaeeyzau2aaSbaaSqaaiabdAgaMnaaBaaameaacqaIXaqmaeqaaaWcbeaaaaa@46CA@ and each protein in S G f 1 MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaem4uamLaem4raC0aaSbaaSqaaiabdAgaMnaaBaaameaacqaIXaqmaeqaaaWcbeaaaaa@30C4@ are aligned by producing A cs P i , where 1 ≤ iQ. The building of HMM f 1 p i MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaeeisaGKaeeyta0Kaeeyta00aaSbaaSqaaiabdAgaMnaaBaaameaacqaIXaqmaeqaaaWcbeaakiabdchaWnaaBaaaleaacqWGPbqAaeqaaaaa@34D1@ classificator is based on A cs P i .

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