Home
last modified time | relevance | path

Searched refs:protein (Results 1 – 25 of 2786) sorted by relevance

12345678910>>...112

/dports/biology/p5-Bio-FeatureIO/Bio-FeatureIO-1.6.905/t/data/
H A Dtest.ptt4 15..2531 + 838 24217062 - LB001 - - hypothetical protein
6 3716..3823 - 35 24217064 - LB004 - - hypothetical protein
7 3779..3886 + 35 24217065 - LB003 - - hypothetical protein
9 4975..5085 + 36 24217067 - LB006 - - hypothetical protein
12 6083..6373 - 96 24217070 - LB009 - - hypothetical protein
21 15186..16169 + 327 24217079 - LB018 - - hypothetical protein
22 16244..16384 + 46 24217080 - LB019 - - hypothetical protein
24 17941..18075 - 44 24217082 - LB021 - - hypothetical protein
28 21008..22150 - 380 24217086 - LB025 - - hypothetical protein
32 24684..24791 - 35 24217090 - LB029 - - hypothetical protein
[all …]
/dports/misc/py-orange3-network/orange3-network-ec534c9/orangecontrib/network/networks/
H A Dleu_huttenhower_a_items.tab5 ACTN1 <=0.00 protein binding
6 ADA >0.00 protein binding
7 ADAM15 <=0.00 protein binding
8 AHR <=0.00 protein binding
11 ANXA2 <=0.00 protein binding
13 AREG <=0.00 protein binding
16 ATRX >0.00 protein binding
17 BARD1 >0.00 protein binding
20 BLK >0.00 protein binding
21 BRF1 >0.00 protein binding
[all …]
/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/libv3/models/protein/
H A Dempirical.bf1 LoadFunctionLibrary("../protein.bf");
8 /** @module models.protein.empirical */
192 __rate_matrix = {models.protein.dimensions,models.protein.dimensions};
258 models.protein.empirical.default_generators = {"LG": "models.protein.LG.ModelDescription",
269 models.protein.empirical.plusF_generators = {"LG": "models.protein.LGF.ModelDescription",
279 models.protein.empirical.mleF_generators = {"LG": "models.protein.LGML.ModelDescription",
312 models.protein.LGF.ModelDescription.model_definition = models.protein.LG.ModelDescription(type);
326 … models.protein.LGML.ModelDescription.model_definition = models.protein.LG.ModelDescription(type);
357 … models.protein.JTTF.ModelDescription.model_definition = models.protein.JTT.ModelDescription(type);
526 models.protein.ABF.ModelDescription.model_definition = models.protein.AB.ModelDescription(type);
[all …]
H A DREV.bf1 LoadFunctionLibrary("../protein.bf");
6 /** @module models.protein.REV */
9 * @name models.protein.REV.ModelDescription
13 lfunction models.protein.REV.ModelDescription(type) {
38 models.protein.REV._generateRate.p = {};
48 …models.protein.REV.parameter_name = parameters.ApplyNameSpace(models.protein.REV.parameter_name, n…
52 …models.protein.REV._generateRate.p[utility.getGlobalValue("terms.model.rate_entry")] = models.prot…
54 return models.protein.REV._generateRate.p;
59 * @name models.protein.REV._DefineQ
98 * @name models.protein.REV.DefineQMatrix
[all …]
/dports/biology/py-biopython/biopython-1.79/Tests/UniProt/
H A Dgp_information.goa_yeast.28.gpi25 A5Z2X5 YPR010C-A UPF0495 protein YPR010C-A YP010_YEAST|YPR010C-A protein taxon:559292 db_subset=S…
26 D6VPM8 YAR023C Putative DUP240 protein YAR023C YAJ3_YEAST|YAR023C protein taxon:559292 db_subset=…
33 E9PAE4 Putative uncharacterized protein E9PAE4_YEAST protein taxon:559292 db_subset=TrEMBL
34 E9PAE7 Putative uncharacterized protein E9PAE7_YEAST protein taxon:559292 db_subset=TrEMBL
35 E9PAE8 Putative uncharacterized protein E9PAE8_YEAST protein taxon:559292 db_subset=TrEMBL
36 E9PAF1 Putative uncharacterized protein E9PAF1_YEAST protein taxon:559292 db_subset=TrEMBL
41 O13511 YAL065C Uncharacterized protein YAL065C YA065_YEAST|YAL065C protein taxon:559292 db_subset…
191 P03871 REP1 Partitioning protein REP1 REP1_YEAST|REP1|R0020C protein taxon:559292 db_subset=Swiss…
192 P03872 REP2 Partitioning protein REP2 REP2_YEAST|REP2|R0040C protein taxon:559292 db_subset=Swiss…
214 P04386 GAL4 Regulatory protein GAL4 GAL4_YEAST|GAL4|YPL248C protein taxon:559292 db_subset=Swiss-…
[all …]
H A Dgoa_yeast.gaf3 !The set of protein accessions included in this file is based on UniProt reference proteomes, which…
13 …003674 GO_REF:0000015 ND F Putative uncharacterized protein YAL019W-A YA19A_YEAST|YAL019W-A prote…
14 …005575 GO_REF:0000015 ND C Putative uncharacterized protein YAL019W-A YA19A_YEAST|YAL019W-A prote…
363 …5 YPR010C-A GO:0003674 GO_REF:0000015 ND F UPF0495 protein YPR010C-A YP010_YEAST|YPR010C-A prote…
364 …5 YPR010C-A GO:0008150 GO_REF:0000015 ND P UPF0495 protein YPR010C-A YP010_YEAST|YPR010C-A prote…
366 …R023C GO:0003674 GO_REF:0000015 ND F Putative DUP240 protein YAR023C YAJ3_YEAST|YAR023C protein
367 …R023C GO:0005575 GO_REF:0000015 ND C Putative DUP240 protein YAR023C YAJ3_YEAST|YAR023C protein
371 …R023C GO:0008150 GO_REF:0000015 ND P Putative DUP240 protein YAR023C YAJ3_YEAST|YAR023C protein
437 …L065C GO:0003674 GO_REF:0000015 ND F Uncharacterized protein YAL065C YA065_YEAST|YAL065C protein
438 …L065C GO:0005575 GO_REF:0000015 ND C Uncharacterized protein YAL065C YA065_YEAST|YAL065C protein
[all …]
H A Dgene_association.goa_yeast.1.gaf32 …000011 PMID:1493335 IMP P Vacuolar protein sorting-associated protein 9 VPS9_YEAST|YML097C|VPT9|V…
39 … GO:0000022 PMID:10465783 TAS P APC/C activator protein CDC20 CDC20_YEAST|YGL116W|CDC20|D6VU31 pr…
72 …1 PMID:1493335 IMP P Vacuolar protein sorting-associated protein 45 VPS45_YEAST|YGL095C|STT10|VPS…
77 …AC8 GO:0000011 PMID:16301533 IMP P Vacuolar protein 8 VAC8_YEAST|YEL013W|VAC8|YEB3|D3DLN6|Q549T0…
78 …VAC8 GO:0000011 PMID:8885233 IMP P Vacuolar protein 8 VAC8_YEAST|YEL013W|VAC8|YEB3|D3DLN6|Q549T0…
99 …7W GO:0000022 PMID:18194531 IMP P Uncharacterized protein YHR127W YHS7_YEAST|YHR127W|D3DL76 prot…
127 … GO:0000027 PMID:15126390 IPI P Ribosome assembly protein 3 RSA3_YEAST|YLR221C|RSA3|D6VYM1 prote…
133 … GO:0000001 PMID:17905927 IMP P Accumulates dyads protein 3 ADY3_YEAST|YDL239C|ADY3|D6VRB7 prote…
176 …11 PMID:1493335 IMP P Vacuolar protein sorting-associated protein 3 VPS3_YEAST|VPS3|YDR495C|VPT17…
179 …3335 IMP P Vacuolar protein sorting-associated protein 21 VPS21_YEAST|YOR089C|VPS12|VPS21|YOR3154…
[all …]
/dports/biology/emboss/EMBOSS-6.6.0/doc/programs/master/emboss/apps/inc/
H A Dextractfeat.output231 … ubiquitin-protein ligase UBR5 (6.3.2.-) (100 kDa protein) (E3 ubiquitin-protein ligase, HECT doma…
233 … ubiquitin-protein ligase UBR5 (6.3.2.-) (100 kDa protein) (E3 ubiquitin-protein ligase, HECT doma…
235 … ubiquitin-protein ligase UBR5 (6.3.2.-) (100 kDa protein) (E3 ubiquitin-protein ligase, HECT doma…
237 … ubiquitin-protein ligase UBR5 (6.3.2.-) (100 kDa protein) (E3 ubiquitin-protein ligase, HECT doma…
239 … ubiquitin-protein ligase UBR5 (6.3.2.-) (100 kDa protein) (E3 ubiquitin-protein ligase, HECT doma…
241 … ubiquitin-protein ligase UBR5 (6.3.2.-) (100 kDa protein) (E3 ubiquitin-protein ligase, HECT doma…
243 … ubiquitin-protein ligase UBR5 (6.3.2.-) (100 kDa protein) (E3 ubiquitin-protein ligase, HECT doma…
245 … ubiquitin-protein ligase UBR5 (6.3.2.-) (100 kDa protein) (E3 ubiquitin-protein ligase, HECT doma…
247 … ubiquitin-protein ligase UBR5 (6.3.2.-) (100 kDa protein) (E3 ubiquitin-protein ligase, HECT doma…
249 … ubiquitin-protein ligase UBR5 (6.3.2.-) (100 kDa protein) (E3 ubiquitin-protein ligase, HECT doma…
[all …]
/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/libv3/models/protein/matrices/
H A Dmt.ibf3 LoadFunctionLibrary("../../protein.bf");
13 * @name models.protein.mtMet.ModelDescription
19 …models.protein.mtMet.ModelDescription.model_definition = models.protein.empirical.ModelDescription…
20 …models.protein.mtMet.ModelDescription.model_definition [terms.model.empirical_rates] = models.prot…
32 …models.protein.mtMetF.ModelDescription.model_definition = models.protein.mtMet.ModelDescription(ty…
45 …models.protein.mtMetML.ModelDescription.model_definition = models.protein.mtMet.ModelDescription(t…
53 models.protein.mtMet.Rij = {
302 …models.protein.mtVerF.ModelDescription.model_definition = models.protein.mtVer.ModelDescription(ty…
315 …models.protein.mtVerML.ModelDescription.model_definition = models.protein.mtVer.ModelDescription(t…
326 models.protein.mtVer.Rij = {
[all …]
H A DHIV.ibf3 LoadFunctionLibrary("../../protein.bf");
15 * @name models.protein.HIVBm.ModelDescription
21 …models.protein.HIVBm.ModelDescription.model_definition = models.protein.empirical.ModelDescription…
22 …models.protein.HIVBm.ModelDescription.model_definition [terms.model.empirical_rates] = models.prot…
34 …models.protein.HIVBmF.ModelDescription.model_definition = models.protein.HIVBm.ModelDescription(ty…
47 …models.protein.HIVBmML.ModelDescription.model_definition = models.protein.HIVBm.ModelDescription(t…
56 models.protein.HIVBm.Rij = {
336 …models.protein.HIVWm.ModelDescription.model_definition = models.protein.empirical.ModelDescription…
349 …models.protein.HIVWmF.ModelDescription.model_definition = models.protein.HIVWm.ModelDescription(ty…
362 …models.protein.HIVWmML.ModelDescription.model_definition = models.protein.HIVWm.ModelDescription(t…
[all …]
H A DJC69.ibf3 LoadFunctionLibrary("../../protein.bf");
12 * @name models.protein.JC69.ModelDescription
18 …models.protein.JC69.ModelDescription.model_definition = models.protein.empirical.ModelDescription(…
19 …models.protein.JC69.ModelDescription.model_definition [terms.model.empirical_rates] = models.prote…
20 …models.protein.JC69.ModelDescription.model_definition [terms.model.frequency_estimator] = "models.
25 * @name models.protein.JC69F.ModelDescription
31 …models.protein.JC69F.ModelDescription.model_definition = models.protein.JC69.ModelDescription(type…
44 …models.protein.JC69ML.ModelDescription.model_definition = models.protein.JC69.ModelDescription(typ…
45 …models.protein.JC69ML.ModelDescription.model_definition [terms.model.frequency_estimator] = "frequ…
51 models.protein.JC69.Rij = {
[all …]
H A DJTT.ibf3 LoadFunctionLibrary("../../protein.bf");
12 * @name models.protein.JTT.ModelDescription
18 …models.protein.JTT.ModelDescription.model_definition = models.protein.empirical.ModelDescription(t…
19 …models.protein.JTT.ModelDescription.model_definition [terms.model.empirical_rates] = models.protei…
20 …models.protein.JTT.ModelDescription.model_definition [terms.model.frequency_estimator] = "models.p…
25 * @name models.protein.JTTF.ModelDescription
31 … models.protein.JTTF.ModelDescription.model_definition = models.protein.JTT.ModelDescription(type);
44 …models.protein.JTTML.ModelDescription.model_definition = models.protein.JTT.ModelDescription(type);
45 …models.protein.JTTML.ModelDescription.model_definition [terms.model.frequency_estimator] = "freque…
51 models.protein.JTT.Rij = {
[all …]
H A DLG.ibf3 LoadFunctionLibrary("../../protein.bf");
12 * @name models.protein.LG.ModelDescription
18 …models.protein.LG.ModelDescription.model_definition = models.protein.empirical.ModelDescription(ty…
19 …models.protein.LG.ModelDescription.model_definition [terms.model.empirical_rates] = models.protein
20 …models.protein.LG.ModelDescription.model_definition [terms.model.frequency_estimator] = "models.pr…
25 * @name models.protein.LGF.ModelDescription
31 models.protein.LGF.ModelDescription.model_definition = models.protein.LG.ModelDescription(type);
44 … models.protein.LGML.ModelDescription.model_definition = models.protein.LG.ModelDescription(type);
45 …models.protein.LGML.ModelDescription.model_definition [terms.model.frequency_estimator] = "frequen…
51 models.protein.LG.Rij = {
[all …]
H A DWAG.ibf3 LoadFunctionLibrary("../../protein.bf");
12 * @name models.protein.WAG.ModelDescription
18 …models.protein.WAG.ModelDescription.model_definition = models.protein.empirical.ModelDescription(t…
19 …models.protein.WAG.ModelDescription.model_definition [terms.model.empirical_rates] = models.protei…
20 …models.protein.WAG.ModelDescription.model_definition [terms.model.frequency_estimator] = "models.p…
25 * @name models.protein.WAGF.ModelDescription
31 … models.protein.WAGF.ModelDescription.model_definition = models.protein.WAG.ModelDescription(type);
44 …models.protein.WAGML.ModelDescription.model_definition = models.protein.WAG.ModelDescription(type);
45 …models.protein.WAGML.ModelDescription.model_definition [terms.model.frequency_estimator] = "freque…
51 models.protein.WAG.Rij = {
[all …]
H A DgcpREV.ibf3 LoadFunctionLibrary("../../protein.bf");
12 * @name models.protein.gcpREV.ModelDescription
18 …models.protein.gcpREV.ModelDescription.model_definition = models.protein.empirical.ModelDescriptio…
19 …models.protein.gcpREV.ModelDescription.model_definition [terms.model.empirical_rates] = models.pro…
20 …models.protein.gcpREV.ModelDescription.model_definition [terms.model.frequency_estimator] = "model…
25 * @name models.protein.gcpREVF.ModelDescription
31 …models.protein.gcpREVF.ModelDescription.model_definition = models.protein.gcpREV.ModelDescription(…
44 …models.protein.gcpREVML.ModelDescription.model_definition = models.protein.gcpREV.ModelDescription…
45 …models.protein.gcpREVML.ModelDescription.model_definition [terms.model.frequency_estimator] = "fre…
51 models.protein.gcpREV.Rij = {
[all …]
/dports/science/py-oddt/oddt-0.7/oddt/scoring/descriptors/
H A D__init__.py130 self.protein = protein
163 self.protein = protein
238 self.protein = protein
260 self.protein = protein
268 out.append(self.func(mol, protein=self.protein))
320 self.protein = protein
331 self.protein = protein
338 protein = self.protein
365 self.protein = protein
385 self.protein = protein
[all …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/writers/unit_test/gff3writer_test_cases/
H A Drw-310.entry.gff3420 …embrane protein (predicted by Phobius);gbkey=mRNA;inference=protein motif:InterPro:IPR019794;locus…
421 …embrane protein (predicted by Phobius);gbkey=mRNA;inference=protein motif:InterPro:IPR019794;locus…
422 …embrane protein (predicted by Phobius);gbkey=mRNA;inference=protein motif:InterPro:IPR019794;locus…
423 …embrane protein (predicted by Phobius);gbkey=mRNA;inference=protein motif:InterPro:IPR019794;locus…
424 …embrane protein (predicted by Phobius);gbkey=mRNA;inference=protein motif:InterPro:IPR019794;locus…
425 …embrane protein (predicted by Phobius);gbkey=mRNA;inference=protein motif:InterPro:IPR019794;locus…
559 …embrane protein (predicted by Phobius);gbkey=mRNA;inference=protein motif:InterPro:IPR024873;locus…
560 …embrane protein (predicted by Phobius);gbkey=mRNA;inference=protein motif:InterPro:IPR024873;locus…
561 …embrane protein (predicted by Phobius);gbkey=mRNA;inference=protein motif:InterPro:IPR024873;locus…
562 …embrane protein (predicted by Phobius);gbkey=mRNA;inference=protein motif:InterPro:IPR024873;locus…
[all …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/blast/seqdb_writer/unit_test/data/
H A Dredundant_deflines.asn3065 title "TIGR01620 family protein [Salmonella enterica]",
3507 title "TIGR01620 family protein [Salmonella enterica]",
3632 title "TIGR01620 family protein [Salmonella enterica]",
3710 title "TIGR01620 family protein [Salmonella enterica]",
3723 title "TIGR01620 family protein [Salmonella enterica]",
3736 title "TIGR01620 family protein [Salmonella enterica]",
3749 title "TIGR01620 family protein [Salmonella enterica]",
14392 title "Membrane protein YcjF [Salmonella enterica]",
16821 title "membrane protein [Escherichia coli]",
16834 title "membrane protein [Escherichia coli]",
[all …]
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/seqdb_writer/unit_test/data/
H A Dredundant_deflines.asn3065 title "TIGR01620 family protein [Salmonella enterica]",
3507 title "TIGR01620 family protein [Salmonella enterica]",
3632 title "TIGR01620 family protein [Salmonella enterica]",
3710 title "TIGR01620 family protein [Salmonella enterica]",
3723 title "TIGR01620 family protein [Salmonella enterica]",
3736 title "TIGR01620 family protein [Salmonella enterica]",
3749 title "TIGR01620 family protein [Salmonella enterica]",
14392 title "Membrane protein YcjF [Salmonella enterica]",
16821 title "membrane protein [Escherichia coli]",
16834 title "membrane protein [Escherichia coli]",
[all …]
/dports/science/py-oddt/oddt-0.7/tests/
H A Dtest_virtualscreening.py202 protein.protein = True
228 vs.score('bad_sf', protein=protein)
231 vs.score('rfscore_v1', protein=protein)
233 vs.score('rfscore_v2', protein=protein)
234 vs.score('rfscore_v3', protein=protein)
235 vs.score('pleclinear', protein=protein)
238 vs.score(filenames[0], protein=protein)
243 vs.score(sum, protein=protein)
257 vs.score('nnscore', protein=protein)
258 vs.score('rfscore_v1', protein=protein)
[all …]
H A Dtest_toolkit.py37 protein.protein = True
73 protein.addh()
79 protein.removeh()
86 protein.removeh()
105 protein.protein = True
124 protein.protein = True
130 protein.addh()
269 rec.protein = True
395 protein.protein = True
412 protein.protein = True
[all …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/writers/unit_test/srcwriter_test_cases/
H A Dtest.srcchk.output3 NP_963295.1 41614797 Nanoarchaeum equitans Kin4-M 228908 Kin4-M hypothetical protein NEQ001…
4 NP_963296.1 41614798 Nanoarchaeum equitans Kin4-M 228908 Kin4-M hypothetical protein NEQ003…
5 NP_963297.1 41614799 Nanoarchaeum equitans Kin4-M 228908 Kin4-M hypothetical protein NEQ002…
6 NP_963298.1 41614800 Nanoarchaeum equitans Kin4-M 228908 Kin4-M hypothetical protein NEQ004…
7 NP_963299.1 41614801 Nanoarchaeum equitans Kin4-M 228908 Kin4-M hypothetical protein NEQ005…
8 NP_963300.1 41614802 Nanoarchaeum equitans Kin4-M 228908 Kin4-M hypothetical protein NEQ007…
9 NP_963301.1 41614803 Nanoarchaeum equitans Kin4-M 228908 Kin4-M hypothetical protein NEQ006…
10 NP_963302.1 41614804 Nanoarchaeum equitans Kin4-M 228908 Kin4-M hypothetical protein NEQ008…
11 NP_963303.1 41614805 Nanoarchaeum equitans Kin4-M 228908 Kin4-M hypothetical protein NEQ009…
12 NP_963304.1 41614806 Nanoarchaeum equitans Kin4-M 228908 Kin4-M hypothetical protein NEQ010…
[all …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/cobalt/unit_test/data/
H A Dlarge.fa4 >gi|49902846|gb|AAH76068.1| Pax6b protein [Danio rerio]
123 >gi|18138024|emb|CAC80514.1| paired box protein [Mus musculus]
135 …PAX-6 protein [Astyanax mexicanus] >gi|2369657|emb|CAA68839.1| PAX-6 protein [Astyanax mexicanus] …
184protein Pax-6 isoform a [Homo sapiens] >gi|189083681|ref|NP_001121084.1| paired box protein Pax-6 …
558 >gi|33585947|gb|AAH55960.1| Pax2-A protein [Xenopus laevis]
1069 >gi|553607|gb|AAC41711.1| paired-box protein [Homo sapiens]
1345 …| paired box protein Pax-2 [Mus musculus] >gi|152012463|gb|AAI50485.1| Pax2 protein [Mus musculus]…
1647 … Full=Paired box protein Pax-2a; AltName: Full=No isthmus protein; AltName: Full=Pax[Zf-b] >gi|437…
1741protein Pax-5 [Xenopus laevis] >gi|82249042|sp|Q9YH95.1|PAX5_XENLA RecName: Full=Paired box protei…
1907 …24307|ref|NP_001079830.1| paired box protein Pax-2-A [Xenopus laevis] >gi|2765059|emb|CAA71207.1| …
[all …]
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/propka30/Source/
H A Doutput.py73 for chain in protein.chains:
119 for chain in protein.chains:
170 str += getSummarySection(protein)
206 printPKASection(protein)
218 str = getSummarySection(protein)
232 for chain in protein.chains:
240 if protein.coupled_residues:
256 for chain in protein.chains:
283 pH, dG = protein.getPHopt()
290 dG_min, dG_max = protein.getDG80()
[all …]
/dports/science/cdk/cdk-cdk-2.3/storage/pdb/src/main/java/org/openscience/cdk/tools/
H A DProteinBuilderTool.java63 addAminoAcid(protein, aaToAdd, strand); in addAminoAcidAtNTerminus()
65 if (protein.getMonomerCount() == 0) { in addAminoAcidAtNTerminus()
71 return protein; in addAminoAcidAtNTerminus()
87 addAminoAcid(protein, aaToAdd, strand); in addAminoAcidAtCTerminus()
95 return protein; in addAminoAcidAtCTerminus()
149 logger.debug("protein: ", protein); in createProtein()
163 protein.addBond(bond); in createProtein()
164 return protein; in createProtein()
169 protein.addAtom(atom, aaToAdd, strand); in addAminoAcid()
171 protein.addBond(bond); in addAminoAcid()
[all …]

12345678910>>...112