PRIMO: An Interactive Homology Modeling Pipeline

Hatherley, Rowan; Brown, David K.; Glenister, Michael; Bishop, Özlem Tastan

doi:10.1371/journal.pone.0166698

Cited by 53 publications

(39 citation statements)

References 41 publications

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“…Table shows current CAMEO data relating the response time to modeling performance. Currently among the fasted servers are SWISS‐MODEL, Phyre2, PRIMO, SPARKS‐X, and Princeton_template all staying below 4 hours to return predictions of high to medium quality. The longest modeling times on average are observed for IntFOLDx‐TS and Robetta, yet these servers are consistently delivering high quality models.…”

Section: Resultsmentioning

confidence: 99%

Continuous Automated Model EvaluatiOn (CAMEO) complementing the critical assessment of structure prediction in CASP12

et al. 2017

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Every second year, the community experiment "Critical Assessment of Techniques for Structure Prediction" (CASP) is conducting an independent blind assessment of structure prediction methods, providing a framework for comparing the performance of different approaches and discussing the latest developments in the field. Yet, developers of automated computational modeling methods clearly benefit from more frequent evaluations based on larger sets of data. The "Continuous Automated Model EvaluatiOn (CAMEO)" platform complements the CASP experiment by conducting fully automated blind prediction assessments based on the weekly pre-release of sequences of those structures, which are going to be published in the next release of the PDB Protein Data Bank. CAMEO publishes weekly benchmarking results based on models collected during a 4-day prediction window, on average assessing ca. 100 targets during a time frame of 5 weeks. CAMEO benchmarking data is generated consistently for all participating methods at the same point in time, enabling developers to benchmark and cross-validate their method's performance, and directly refer to the benchmarking results in publications. In order to facilitate server development and promote shorter release cycles, CAMEO sends weekly email with submission statistics and low performance warnings. Many participants of CASP have successfully employed CAMEO when preparing their methods for upcoming community experiments. CAMEO offers a variety of scores to allow benchmarking diverse aspects of structure prediction methods. By introducing new scoring schemes, CAMEO facilitates new development in areas of active research, for example, modeling quaternary structure, complexes, or ligand binding sites.

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Section: Resultsmentioning

confidence: 99%

Continuous Automated Model EvaluatiOn (CAMEO) complementing the critical assessment of structure prediction in CASP12

et al. 2017

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“…Here, “SWISS‐MODEL” (69.09±10.33 lDDT, 0.69 CAD‐score, 99% of medium targets), “IntFOLD3‐TS” (69.21±7.40 lDDT, 0.69 CAD‐score, 98% of medium targets), and “HHPredB” (68.31±9.60 lDDT, 0.68 CAD‐score, 100% medium targets) are close with regard to performance. “SWISS‐MODEL” is sticking out with a very fast average response time of 12 minutes, closely followed by “HHPredB” (42 minutes), “PRIMO” (54 minutes), and “SPARKS‐X” (114 minutes). For the easy targets (in total 47), 12 out of 16 servers showed lDDT scores in the range of 80 to 84, with “Robetta” (lDDT 84.55±4.04) and “SWISS‐MODEL” (lDDT 83.88±5.38) in a narrow lead.…”

Section: Resultsmentioning

confidence: 99%

Introducing “best single template” models as reference baseline for the Continuous Automated Model Evaluation (CAMEO)

et al. 2019

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Critical blind assessment of structure prediction techniques is crucial for the scientific community to establish the state of the art, identify bottlenecks, and guide future developments. In Critical Assessment of Techniques in Structure Prediction (CASP), human experts assess the performance of participating methods in relation to the difficulty of the prediction task in a biennial experiment on approximately 100 targets. Yet, the development of automated computational modeling methods requires more frequent evaluation cycles and larger sets of data. The “Continuous Automated Model EvaluatiOn (CAMEO)” platform complements CASP by conducting fully automated blind prediction evaluations based on the weekly pre‐release of sequences of those structures, which are going to be published in the next release of the Protein Data Bank (PDB). Each week, CAMEO publishes benchmarking results for predictions corresponding to a set of about 20 targets collected during a 4‐day prediction window. CAMEO benchmarking data are generated consistently for all methods at the same point in time, enabling developers to cross‐validate their method's performance, and referring to their results in publications. Many successful participants of CASP have used CAMEO—either by directly benchmarking their methods within the system or by comparing their own performance to CAMEO reference data. CAMEO offers a variety of scores reflecting different aspects of structure modeling, for example, binding site accuracy, homo‐oligomer interface quality, or accuracy of local model confidence estimates. By introducing the "bestSingleTemplate" method based on structure superpositions as a reference for the accuracy of 3D modeling predictions, CAMEO facilitates objective comparison of techniques and fosters the development of advanced methods.

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“…The 3D structure of AQP1 was modeled using PRotein Interactive MOdeling (PRIMO) pipeline (https://primo.rubi.ru.ac.za) (using default settings) [28]. Structures with identity percent higher than 30% were selected as suitable template model structures.…”

Section: Methodsmentioning

confidence: 99%

In Silico Analysis of Ixodid Tick Aqauporin-1 Protein as a Candidate Anti-Tick Vaccine Antigen

Ndekezi

Nkamwesiga

Ochwo

et al. 2019

Preprint

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21Ticks are arthropod vectors of pathogens of both Veterinary and Public health importance.22 Ticks are largely controlled by acaricide application. However, acaricide efficacy is hampered by 23 high cost, the need for regular application and selection of multi-acaricide resistant tick 24 populations. In light of this, future tick control approaches are poised to rely on integration of 25 rational acaricide application and other methods such as vaccination. To contribute to systematic 26 research-guided efforts to produce anti-tick vaccines, we carried out an in silico tick Aquaporin-1 27 protein (AQP1) analysis to identify unique tick AQP1 peptide motifs that can be used in future 28 peptide anti-tick vaccine development. We used multiple sequence alignment (MSA), motif 29 analysis, homology modeling, and structural analysis to identify unique tick AQP1 peptide motifs. 30 BepiPred, Chou & Fasman-Turn, Karplus & Schulz Flexibility and Parker-Hydrophilicity 31 prediction models were used to asses these motifs' abilities to induce antibody mediated immune 32 responses. Tick AQP1 (MK334178) protein homology was largely similar to the bovine AQP1 33 (PDB:1J4N) (23 % sequence similarity; Structural superimposition RMS=1.475). The highest 34 similarities were observed in the transmembrane domains while differences were observed in the 35 extra and intra cellular protein loops. Two unique tick AQP1 (MK334178) motifs, M7 (residues 36 106-125, p=5.4e-25) and M8 (residues 85-104, p=3.3e-24) were identified. These two motifs are 37 located on the extra-cellular AQP1 domain and showed the highest Parker-Hydrophilicity 38 prediction immunogenic scores of 1.153 and 2.612 respectively. The M7 and M8 motifs are a good 39 starting point for the development of potential peptide-based anti-tick vaccine. Further analyses 40 such as in vivo immunization assays are required to validate these findings. 41 42 Key words: Aquaporin-1 protein, Immunogenicity; Tick control; Peptide motifs 3 43 Background 44 Ticks are arthropod vectors of pathogens of both Veterinary and Public health concern in 45 tropical and sub-tropical regions of the world [1,2]. In 2007, the average annual cost of tick borne 46 diseases (TBDs) management was estimated to be 4.20 US Dollars per head of cattle [3]. Ticks 47 are associated with both direct and indirect constraints to livestock health and production [1,2].48 Their direct constraints to livestock production include, but are not limited to, blood loss (anemia), 49 discomfort, skin-and-hide quality loss, and tick paralysis (Fig 1) [4]. Their indirect constraints to 50 livestock production and health relate to transmission of diseases of veterinary importance 51 including: anaplasmosis (Anaplasma spp), babesiosis (Babesia spp), theileriosis (Theileria spp.), 52 and heartwater (Cowdria ruminatium) [1]. In addition, ticks transmit zoonotic pathogens belonging 53 to Babesia spp., Borrelia spp., Rickettsia spp., Ehrlichia spp., Francisella tularensis, Coxiella 54 burnetii, and viruses such as Nairovirus (Bunyaviri...

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PRIMO: An Interactive Homology Modeling Pipeline

Cited by 53 publications

References 41 publications

Continuous Automated Model EvaluatiOn (CAMEO) complementing the critical assessment of structure prediction in CASP12

Continuous Automated Model EvaluatiOn (CAMEO) complementing the critical assessment of structure prediction in CASP12

Introducing “best single template” models as reference baseline for the Continuous Automated Model Evaluation (CAMEO)

In Silico Analysis of Ixodid Tick Aqauporin-1 Protein as a Candidate Anti-Tick Vaccine Antigen

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