WeFold_CASP12

The wfRstta-PQ2-Seder Branch

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E. Faraggi and A. Kloczkowski We have participated in the Critical Assessment of Protein Structure Prediction (CASP) experiment with four prediction procedures. The procedure described in this abstract is labeled as group “wfRstta-PQ2-Seder”, number 067. This method is based on new version of the Seder program [1,2], with new and improved input features as will be described in an upcoming manuscript. For this procedure Seder was trained with soft and hard protein targets. We use CASP5 through CASP10 server models for training data, and CASP11 server models as a test…read more

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The wfCPUNK Branch

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Prediction of protein structure with the UNRES force field aided by secondary-structure and contact prediction A.G. Lipska1, P. Krupa2, M.A. Mozolewska2, A.K. Sieradzan1, C. Kieslich3, M. Onel3, U. Shah3, Y. He2, Y. Yin2, Ł. Golon1, R. Ślusarz1, M. Ślusarz1, A. Liwo1, C.A. Floudas3, H.A. Scheraga2 and S.N. Crivelli4* 1 – Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland, 2 -Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853-1301, U.S.A., 3 – Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX…read more

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The wfAll-Cheng Branch

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Tertiary Structure Prediction by wfAll-Cheng Jie Hou1, Badri Adhikari1, Renzhi Cao2, Silvia Crivelli3, and Jianlin Cheng1* 1 – Department of Computer Science, University of Missouri, Columbia, MO 65211, USA, 2 – Department of Computer Science, Pacific Lutheran University, WA 98447, USA, 3 – Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA *chengji@missouri.edu WeFold [1] is a community-wide cooperation project for protein structure prediction within CASP. As part of the WeFold collaborative, we evaluated all of the WeFold models generated by other WeFold branches and selected 5 top ranked models, followed…read more

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The wfDB_BW_SVGroup Branch

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Assessing Protein Structure Models using Protein Structure Networks [PSN-QA] B.K. Dhanasekaran, Sambit Ghosh, Saraswathi Vishveshwara, Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India, and the WeFold Community, https://wefold.nersc.gov/wordpress/ sv@mbu.iisc.ernet.in WeFold is an open collaboration initiative for protein structure prediction within CASP. It brings together labs and individuals through the science gateway http://wefold.nersc.gov/ and provides computing and storage resources through the National Energy Research Scientific Computing (NERSC) center. WeFold enables the interaction among groups that work on different components of the protein structure prediction pipeline, thus making it possible to…read more

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The wfMESHI-TIGRESS Branch

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WeFold – the wfMESHI-TIGRESS branch Tomer Sidi and Chen Keasar, Ben-Gurion University of the Negev, Israel, Melis Onel, Utkarsh Shah, Chris Kieslich, and Christodoulos A. Floudas, Texas A&M University, USA, and S.N. Crivelli, Lawrence Berkeley National Laboratory, USA chris.kieslich@gmail.com WeFold [1] is an open collaboration initiative for protein structure prediction within CASP. It brings together labs and individuals through the science gateway http://wefold.nersc.gov/ and provides computing and storage resources through the National Energy Research Scientific Computing (NERSC) center. WeFold enables the interaction among groups that work on different components of…read more

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The wfMESHI-Seok Branch

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WeFold – the wfMESHI-Seok branch T. Sidi and C. Keasar, Ben-Gurion University of the Negev, Israel, and Lim Heo, Gyu Rie Lee, Minkyung Baek, and Chaok Seok, Department of Chemistry, Seoul National University, Seoul 151-747, Republic of Korea chaok@snu.ac.kr WeFold is an open collaboration initiative for protein structure prediction within CASP. It brings together labs and individuals through the science gateway http://wefold.nersc.gov/ and provides computing and storage resources through the National Energy Research Scientific Computing (NERSC) center. WeFold enables the interaction among groups that work on different components of the…read more

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The wf-BAKER-UNRES Branch

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Prediction of protein structure with the UNRES force field aided by contact- and secondary-structure prediction derived from evolutionarily related proteins A.G. Lipska, M.A. Mozolewska, P. Krupa, R. Ślusarz, M. Ślusarz, and A. Liwo, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland, M.D. Wiśniewska, Centre of New Technologies, University of Warsaw, Banacha 2c Str., 02-097 Warsaw, Poland, S. Ovchinnikov and D. Baker, Department of Biochemistry, and Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA, and S.N. Crivelli, Department of Computer Science, UC Davis,…read more

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The wfRosetta-MUfold Branch

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Protein structure refinements by using MUfold to sample Rosetta decoys Hongbo Li, School of Computer Science and Information Technology, NorthEast Normal University, Changchun, 130117, China, and Department of Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65211, USA, and Dong Xu, Department of Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65211, USA. xudong@missouri.edu A number of effective tools for protein structure prediction, such as I-TASSER, Modeller and Rosetta have been developed. These tools often generate many models…read more

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The wfRstta-PQ-MESHI-MSC Branch

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Selection of Rosetta decoys using ProQ2 and MESHI-MSC S. Mirzaei, California State Polytechnic University, Pomona; Industrial and Manufacturing Engineering Department, USA, T. Sidi and C. Keasar, Department of Computer Science, Ben-Gurion University of the Negev, Israel, D. E. Kim and D. Baker, Dept. of Biochemistry, University of Washington, USA, B. Wallner, Division of Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden, and S.N. Crivelli, Lawrence Berkeley National Laboratory, USA sncrivelli@lbl.gov WeFold is an open collaboration initiative for protein structure prediction within CASP. It brings together researchers through…read more

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The wfRosetta-ProQ-MESHI Branch

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WeFold – the wfRosetta-ProQ-MESHI pipeline T. Sidi and C. Keasar, Department of Computer Science, Ben-Gurion University of the Negev, Israel, D. E. Kim and D. Baker, Institute for Protein Design, University of Washington, USA, B. Wallner, Division of Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Sweden, and S.N. Crivelli, Lawrence Berkeley National Laboratory, USA chen@cs.bgu.ac.il WeFold is an open collaboration initiative for protein structure prediction within CASP. It brings together researchers through the science gateway http://wefold.nersc.gov/ and provides computing and storage resources through the National Energy Research Scientific…read more

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