Journal: Journal of chemical information and modeling

Article Title: FINDSITE comb2.0 : A New Approach for Virtual Ligand Screening of Proteins and Virtual Target Screening of Biomolecules

doi: 10.1021/acs.jcim.8b00309

Figure Lengend Snippet: Comparison between FINDSITE comb2.0 and FINDSITE comb on the DUD-E set

Article Snippet: FINDSITE comb has also been demonstrated to outperform state-of-the-art docking methods such as DOCK6 5 and AUTODOCK-vina 8 and shows comparable accuracy when low resolution predicted or experimental structures are used.

Techniques: Comparison

Journal: Journal of chemical information and modeling

Article Title: FINDSITE comb2.0 : A New Approach for Virtual Ligand Screening of Proteins and Virtual Target Screening of Biomolecules

doi: 10.1021/acs.jcim.8b00309

Figure Lengend Snippet: Comparison of FINDSITE comb2.0 with CNN methods on the DUD-E set

Article Snippet: FINDSITE comb has also been demonstrated to outperform state-of-the-art docking methods such as DOCK6 5 and AUTODOCK-vina 8 and shows comparable accuracy when low resolution predicted or experimental structures are used.

Techniques: Comparison

Journal: Journal of chemical information and modeling

Article Title: FINDSITE comb2.0 : A New Approach for Virtual Ligand Screening of Proteins and Virtual Target Screening of Biomolecules

doi: 10.1021/acs.jcim.8b00309

Figure Lengend Snippet: Comparison between FINDSITE comb2.0 and FINDSITE comb for drug target prediction

Article Snippet: FINDSITE comb has also been demonstrated to outperform state-of-the-art docking methods such as DOCK6 5 and AUTODOCK-vina 8 and shows comparable accuracy when low resolution predicted or experimental structures are used.

Techniques: Comparison

Journal: Journal of Fungi

Article Title: Diversity of Sordariales Fungi: Identification of Seven New Species of Naviculisporaceae Through Morphological Analyses and Genome Sequencing

doi: 10.3390/jof11120880

Figure Lengend Snippet: ITS + LSU phylogenetic tree of the Naviculisporaceae . The tree was rooted with Apodospora peruviana CBS 118,394. The strains whose genome sequences were obtained in the present study are shown in red, and the strains whose genome sequences were previously published are in blue . On the left panel, Ts indicate ex-type strains. Insets show cladograms of Rhypophila and Pseudorhypophila displaying bootstrap values.

Article Snippet: PSQ110 , Pseudorhypophila latipes comb. nov. , 2019 , Québec, Canada , Soil , Novogene , 52.6 , homothallic.

Techniques:

Journal: Journal of Fungi

Article Title: Diversity of Sordariales Fungi: Identification of Seven New Species of Naviculisporaceae Through Morphological Analyses and Genome Sequencing

doi: 10.3390/jof11120880

Figure Lengend Snippet: Morphology of Pseudorhypophila latipes comb. nov. IMI350600. Mycelium on M2 medium after two weeks of growth ( A ). Perithecia, non-ostiolate, were readily differentiated on M2 and M0 + miscanthus after 2–3 weeks incubation at 27 °C with constant illumination, superficial or immersed, black, globose to subglobose, and they were 449 ± 89 µm diam ( n = 10) ( B , C ); their peridium was pale brown and semi-translucid, tissue type was textura angularis ( D ). Asci were eight-spored, and clavate with a tapering and narrow apex ( E – G ). Ascospores were biseriate and bicellular ( G ). Ascospore heads were 18.0 ± 0.8 × 10.6 ± 0.5 µm ( n = 30), ovoid with a slightly flattened base, and hyaline at first ( I ), then green ( J ) and brown to dark brown when matured ( H , I , K ). The primary appendage was a rounded head and hyaline ( J ), frequently collapsing at maturity ( K ), they were 4.5 ± 0.6 × 6.4 ± 0.6 µm ( n = 10). This description fits the original description of Lundqvist (as Tripterospora latipes: perithecium = 290–700 µm diam, spore head = 15.5–20.5 × 10–13 µm, primary appendage = 6.3–7.7 × 5.5–7 µm; ). Scale bars: B = 200 µm; C = 100 µm; D , E = 20 µm; F – K = 10 µm.

Article Snippet: PSQ110 , Pseudorhypophila latipes comb. nov. , 2019 , Québec, Canada , Soil , Novogene , 52.6 , homothallic.

Techniques: Incubation

Journal: Journal of Fungi

Article Title: Diversity of Sordariales Fungi: Identification of Seven New Species of Naviculisporaceae Through Morphological Analyses and Genome Sequencing

doi: 10.3390/jof11120880

Figure Lengend Snippet: Morphology of Pseudorhypophila oryzae PSN2009. Mycelium on M2 medium after two weeks of growth ( A , B ). Non-ostiolate perithecia were readily differentiated on M0 + miscanthus after 2–3 weeks incubation at 27 °C with constant illumination; pyriform, superficial or semi-immersed, 415 ± 107 µm diam ( n = 10) ( C , D ). Their peridium was pale brown and semi-translucid, and tissue type was textura angularis . ( E , F ). Paraphyses absent. Asci were eight-spored, clavate with a tapering and narrow apex ( G ). Ascospores were uniseriate in young asci and were disordered in older ones ( G , H ). Ascospore heads were 21.7 ± 2.2 × 13.2 ± 1.1 μm ( n = 30), ellipsoidal to oval, and hyaline at first, then green and brown to dark brown when matured ( I – K ). Few ascospores (less than 10%) were 1-septate (septum slightly curved or straight toward the apex), with one cell 12.4 ± 1.9 µm and the other 8.5 ± 1.8 μm ( n = 15) ( I – K ). This description fits with that of A. oryzae Carolis and Arx (non-ostiolate perithecium = 200–500 µm; ascospore = 21–27 × 10–14 µm, more than 90% of the ascospores remaining single-celled; ). Scale bars: C = 200 µm; D = 100 µm; E – H = 20 µm; I – K = 10 µm.

Article Snippet: PSQ110 , Pseudorhypophila latipes comb. nov. , 2019 , Québec, Canada , Soil , Novogene , 52.6 , homothallic.

Techniques: Incubation

Journal: Journal of Fungi

Article Title: Diversity of Sordariales Fungi: Identification of Seven New Species of Naviculisporaceae Through Morphological Analyses and Genome Sequencing

doi: 10.3390/jof11120880

Figure Lengend Snippet: Morphology of Pseudorhypophila mangenotii IMI229747. Mycelium on OA medium after two weeks of growth ( A ). Perithecia were readily differentiated on OA after 2–3 weeks incubation at 27 °C with constant illumination, immersed or semi-immersed, black; they were 266 ± 47 µm diam ( n = 10) ( B , C ), with a clearly defined and narrow neck ( B , F ). Their peridium was pale brown and semi-translucid, and tissue type was textura angularis ( D , E ). Asci were eight-spored, clavate with a tapering and narrow apex ( G , H ). Ascospores were biseriate and bicellular ( G – I ). Ascospore heads were 15.8 ± 0.9 × 8.0 ± 0.4 µm (height × base size; n = 30), oval with a slightly flattened base, and hyaline at first ( G , I , J ), then green ( I ) and black when matured ( I , J ). The primary appendage shape had a rounded end and was hyaline ( I , J ), and they were 5.7 ± 0.5 × 7.9 ± 0.4 µm ( n = 10). This description fits the original one made by von Arx and Hennebert (as Triangularia mangenotii : perithecium = 170–260 µm diam., ascospore size = 21–24 × 7–9 µm, primary appendage = 7–9 µm diam.; ). Scale bars: B , C = 200 µm; D – I = 20 µm; J = 10 µm.

Article Snippet: PSQ110 , Pseudorhypophila latipes comb. nov. , 2019 , Québec, Canada , Soil , Novogene , 52.6 , homothallic.

Techniques: Incubation

Journal: Journal of Fungi

Article Title: Diversity of Sordariales Fungi: Identification of Seven New Species of Naviculisporaceae Through Morphological Analyses and Genome Sequencing

doi: 10.3390/jof11120880

Figure Lengend Snippet: Morphology of Pseudorhypophila marina IMI229743. Mycelium on medium after two weeks of growth ( A , B ). Perithecia, non-ostiolate, were readily differentiated on M2, M0 + miscanthus, OA, V8 and M0 + hay after 2–3 weeks incubation at 27 °C with constant illumination, superficial or immersed, black, globose to subglobose, and they were 287 ± 20 µm diam ( n = 10) ( C , D ). Their peridium was pale brown and semi-translucid, tissue type was textura angularis ( E , F ). Asci were eight-spored, clavate with a tapering and narrow apex ( G , H ). Ascospores were biseriate and bicellular ( G – I ). Ascospore heads were 17.7 ± 0.9 × 12.2 ± 0.5 µm ( n = 30), oval with a slightly flattened base or somewhat truncate base, and hyaline at first ( G , H , J ), then green ( J , K ) and brown to dark brown when matured ( J , L ). The primary appendage was semi-long and flat, hyaline, frequently collapsing ( J – L ), and they were 12.2 ± 4 × 5.2 ± 1.3 ( n = 10). IMI229743 (=NHL 2731) is the ex-type strain for P. marina and this description fits the original one made by Furuya and Udagawa (as Zopfiella marina : perithecium = 180–450 µm, ascospore head = (14–)15–20 × 10–13(–14) µm, primary appendage = 8–10 × 3–4 µm; ). Scale bars: C , D = 100 µm; E – H = 20 µm; I – L = 10 µm.

Article Snippet: PSQ110 , Pseudorhypophila latipes comb. nov. , 2019 , Québec, Canada , Soil , Novogene , 52.6 , homothallic.

Techniques: Incubation

Journal: Journal of Fungi

Article Title: Diversity of Sordariales Fungi: Identification of Seven New Species of Naviculisporaceae Through Morphological Analyses and Genome Sequencing

doi: 10.3390/jof11120880

Figure Lengend Snippet: Morphology of Pseudorhypophila gallica sp. nov. PSN540. Mycelium on M2 medium after two weeks of growth ( A ). Perithecia ( B ). Perithecium wall is textura angularis ( C , D ). Asci and ascospores ( G , H ). Asci ( E ) and ascospores ( F – I ). Scale bars: B = 400 µm; C – E = 20 µm; G – I = 10 µm.

Article Snippet: PSQ110 , Pseudorhypophila latipes comb. nov. , 2019 , Québec, Canada , Soil , Novogene , 52.6 , homothallic.

Techniques:

Journal: Journal of Fungi

Article Title: Diversity of Sordariales Fungi: Identification of Seven New Species of Naviculisporaceae Through Morphological Analyses and Genome Sequencing

doi: 10.3390/jof11120880

Figure Lengend Snippet: Morphology of Pseudorhypophila guyanensis sp. nov. PSN2406. Mycelium on M2 medium after two weeks of growth ( A ). Perithecia ( B ). Peridium with textura angularis ( C ). Young asci ( D ). Mature asci with ascospores ( E , F ). Young ascospores ( G – I ). Mature ascospores ( J ). Scale bars: B = 200 µm; C – F , J = 20 µm; G , I = 10 µm.

Article Snippet: PSQ110 , Pseudorhypophila latipes comb. nov. , 2019 , Québec, Canada , Soil , Novogene , 52.6 , homothallic.

Techniques: