Cloud Prediction of Protein Structure and Function with PredictProtein for Debian

Kaján, László; Yachdav, Guy; Vicedo, Esmeralda; Steinegger, Martin; Mirdita, Milot; Angermüller, Christof; Böhm, Ariane; Domke, Simon; Ertl, Julia; Mertes, Christian; Reisinger, Eva; Staniewski, Cedric; Rost, Burkhard

doi:10.1155/2013/398968

Cited by 16 publications

(11 citation statements)

References 39 publications

(38 reference statements)

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“…Benchmarking of the evfold prediction by secondary structure predictors was done using phyre2 , raptorx , and i‐tasser and by topology predictors: hmmtop , tmpred , Predicts protein , and topcons ; the output of the latter program is a consensus based on polyphobius , octopus , phillius , scampi , and spoctopus . A one was assigned if an amino acid was predicted to be part of an α‐helix or transmembrane segment.…”

Section: Methodsmentioning

confidence: 99%

“…The retrieved PDB file was analyzed using PYMOL (The PyMOL Molecular Graphics System, Version 1.5.0.4 Schr€ odinger, LLC, Mannheim, Germany). Benchmarking of the EVFOLD prediction by secondary structure predictors was done using PHYRE2 [56], RAPTORX [57], and I-TASSER [58] and by topology predictors: HMMTOP [59], TMPRED [60], Predicts protein [61], and TOPCONS [55]; the output of the latter program is a consensus based on POLYPHOBIUS, OCTOPUS, PHILLIUS, SCAMPI, and SPOCTOPUS. A one was assigned if an amino acid was predicted to be part of an a-helix or transmembrane segment.…”

Section: Topology Modelingmentioning

confidence: 99%

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Extracellular loops matter – subcellular location and function of the lysine transporter Lyp1 from Saccharomyces cerevisiae

et al. 2020

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Yeast amino acid transporters of the APC superfamily are responsible for the proton motive force-driven uptake of amino acids into the cell, which for most secondary transporters is a reversible process. The L-lysine proton symporter Lyp1 of Saccharomyces cerevisiae is special in that the Michaelis constant from out-to-in transport (K out!in m) is much lower than K in!out m , which allows accumulation of L-lysine to submolar concentration. It has been proposed that high intracellular lysine is part of the antioxidant mechanism of the cell. The molecular basis for the unique kinetic properties of Lyp1 is unknown. We compared the sequence of Lyp1 with APC para-and orthologues and find structural features that set Lyp1 apart, including differences in extracellular loop regions. We screened the extracellular loops by alanine mutagenesis and determined Lyp1 localization and activity and find positions that affect either the localization or activity of Lyp1. Half of the affected mutants are located in the extension of extracellular loop 3 or in a predicted a-helix in extracellular loop 4. Our data indicate that extracellular loops not only connect the transmembrane helices but also serve functionally important roles.

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Section: Methodsmentioning

confidence: 99%

Section: Topology Modelingmentioning

confidence: 99%

Extracellular loops matter – subcellular location and function of the lysine transporter Lyp1 from Saccharomyces cerevisiae

et al. 2020

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“…Users with access to cloud computing can download the PredictProtein Machine Image or PPMI (60), a disk image optimized for deployment in the cloud. The PPMI is bootable on server instances in cloud infrastructure services, or on locally installed virtualization software.…”

Section: Web Server—updates and Softwarementioning

confidence: 99%

PredictProtein—an open resource for online prediction of protein structural and functional features

Yachdav

Kloppmann

Kaján

et al. 2014

Nucleic Acids Research

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558

438

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PredictProtein is a meta-service for sequence analysis that has been predicting structural and functional features of proteins since 1992. Queried with a protein sequence it returns: multiple sequence alignments, predicted aspects of structure (secondary structure, solvent accessibility, transmembrane helices (TMSEG) and strands, coiled-coil regions, disulfide bonds and disordered regions) and function. The service incorporates analysis methods for the identification of functional regions (ConSurf), homology-based inference of Gene Ontology terms (metastudent), comprehensive subcellular localization prediction (LocTree3), protein–protein binding sites (ISIS2), protein–polynucleotide binding sites (SomeNA) and predictions of the effect of point mutations (non-synonymous SNPs) on protein function (SNAP2). Our goal has always been to develop a system optimized to meet the demands of experimentalists not highly experienced in bioinformatics. To this end, the PredictProtein results are presented as both text and a series of intuitive, interactive and visually appealing figures. The web server and sources are available at http://ppopen.rostlab.org.

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“…The integration of a single software package can trigger a collection of multiple other software tools to be packaged together to complete common workflows in that field. For example, porting of the GenomeTools software suite [ 21 ] during the 2012 Debian Med Sprint not only integrated a substantial number of published and established sequence analysis tools into Debian, but also paved the way for future inclusion of packages dependent on the associated GenomeTools library, e.g., ParsEval [ 22 ] or LTRsift [ 23 ] or the wealth of PredictProtein [ 24 ]. This emphasizes the role of Sprints as strong promoters of synergistic effects within the community.…”

Section: Methodsmentioning

confidence: 99%

Community-driven development for computational biology at Sprints, Hackathons and Codefests

et al. 2014

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BackgroundComputational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools for its interpretation can find mutual understanding and consensus. Much conversation and joint investigation are required in order to identify and implement the best approaches.Traditionally, scientific conferences feature talks presenting novel technologies or insights, followed up by informal discussions during coffee breaks. In multi-institution collaborations, in order to reach agreement on implementation details or to transfer deeper insights in a technology and practical skills, a representative of one group typically visits the other. However, this does not scale well when the number of technologies or research groups is large.Conferences have responded to this issue by introducing Birds-of-a-Feather (BoF) sessions, which offer an opportunity for individuals with common interests to intensify their interaction. However, parallel BoF sessions often make it hard for participants to join multiple BoFs and find common ground between the different technologies, and BoFs are generally too short to allow time for participants to program together.ResultsThis report summarises our experience with computational biology Codefests, Hackathons and Sprints, which are interactive developer meetings. They are structured to reduce the limitations of traditional scientific meetings described above by strengthening the interaction among peers and letting the participants determine the schedule and topics. These meetings are commonly run as loosely scheduled "unconferences" (self-organized identification of participants and topics for meetings) over at least two days, with early introductory talks to welcome and organize contributors, followed by intensive collaborative coding sessions. We summarise some prominent achievements of those meetings and describe differences in how these are organised, how their audience is addressed, and their outreach to their respective communities.ConclusionsHackathons, Codefests and Sprints share a stimulating atmosphere that encourages participants to jointly brainstorm and tackle problems of shared interest in a self-driven proactive environment, as well as providing an opportunity for new participants to get involved in collaborative projects.

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Cloud Prediction of Protein Structure and Function with PredictProtein for Debian

Cited by 16 publications

References 39 publications

Extracellular loops matter – subcellular location and function of the lysine transporter Lyp1 from Saccharomyces cerevisiae

Extracellular loops matter – subcellular location and function of the lysine transporter Lyp1 from Saccharomyces cerevisiae

PredictProtein—an open resource for online prediction of protein structural and functional features

Community-driven development for computational biology at Sprints, Hackathons and Codefests

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