Outcome of a Workshop on Applications of Protein Models in Biomedical Research

By Torsten Schwede, Andrej Sali, Barry Honig, Michael Levitt, Helen M. Berman, David T. Jones, Steven E. Brenner, Stephen K. Burley, Rhiju Das, N. V. Dokholyan and 22 more. 2009

145 citations recorded by the source corpus.

Summary We describe the proceedings and conclusions from a “Workshop on Applications of Protein Models in Biomedical Research” that was held at University of California at San Francisco on 11 and 12 July, 2008. At the workshop, international scientists involved with structure modeling explored (i) how models are currently used in biomedical research, (ii) what the requirements and challenges for different applications are, and (iii) how the interaction between the computational and experimental research communities could be strengthened to advance the field.

Subfields: Molecular Biology, Radiology, Nuclear Medicine and Imaging, Computational Biology & Bioinformatics, Medical & Health AI

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

In Radiology, Nuclear Medicine and Imaging

In Computational Biology & Bioinformatics

Citations in the corpus

Introducing “best single template” models as reference baseline for the Continuous Automated Model Evaluation (CAMEO) (2019, methodology): “models in life science research requires fully automated, robust, reliable, and accurate modeling pipelines.(1) However, the performance”
SWISS-MODEL: homology modelling of protein structures and complexes (2018, neutral): “SWISS-MODEL is optimized for comparative protein modelling cases, where high-quality models can be generated and used in a variety of practical research applications (62).”
The SWISS-MODEL Repository—new features and functionality (2016, background): “Ultimately, the requirements of a specific application determine if a model at hand is suitable for the intended purpose (30).”
Toward the estimation of the absolute quality of individual protein structure models (2010, background): “Received on August 27, 2010; revised on November 3, 2010; accepted on November 29, 2010”
Assessment of the assessment: Evaluation of the model quality estimates in CASP10 (2013, methodology): “Confidence estimates are converted to the (0;1) range using the S-score like equation (1) and the correspondence between the true and false positive rates of all the QA2 predictors is plotted for different predictive thresholds.”
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information (2014, methodology): “An indispensable part of every modelling procedure is the estimation of a protein model’s accuracy, directly providing the user with information regarding the range of its possible applications (11,20,21).”
The Protein Model Portal—a comprehensive resource for protein structure and model information (2013, background): “Because the accuracy requirements for different scientific applications vary (11), CAMEO offers a variety of scores assessing different aspects of a prediction (coverage, local accuracy, completeness, responsiveness, etc.”
Methods of model accuracy estimation can help selecting the best models from decoy sets: assessment of model accuracy estimations in CASP11 (2015, methodology): “Accuracy estimation methods in CASP11 were evaluated in three subcategories: (1) QAglob: estimation of the global accuracy of models (33 QA groups assessed), where a single score is assigned to a model, (2) QAloc: estimation of the local accuracy of models (21 QA groups assessed), where each residue”
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop (2015, unknown): “In addition, the wwPDB and, in later years, the Structural Biology Knowledgebase (SBKB), spearheaded three workshops focused on validation, archiving, and dissemination of comparative protein structure models (Berman et al., 2006; Schwede et al., 2009).”
Automated Minimization of Steric Clashes in Protein Structures (2011, background): “4 However, all-atom structural modeling of proteins requires stringent quality control to ensure that the structures are physically accurate.”
Evaluation of model quality predictions in CASP9 (2011, methodology): “To test whether Pearson’s correlation coefficients r1 and r2 from two different samples are significantly different, we converted them into the corresponding Fisher’s Z1 and Z2 using formula (1) and then computed a statistics Z by dividing their absolute difference by the pooled standard error, that”
Protein structure modeling with MODELLER. (2014, background): “In the absence of experimentally determined structures, computationally derived protein structure models are often valuable for generating testable hypotheses(3,4).”