Search Results for author: Renzhi Cao

Found 6 papers, 2 papers with code

Artificial Intelligence Advances for De Novo Molecular Structure Modeling in Cryo-EM

no code implementations11 Feb 2021 Dong Si, Andrew Nakamura, Runbang Tang, Haowen Guan, Jie Hou, Ammaar Firozi, Renzhi Cao, Kyle Hippe, Minglei Zhao

Cryo-electron microscopy (cryo-EM) has become a major experimental technique to determine the structures of large protein complexes and molecular assemblies, as evidenced by the 2017 Nobel Prize.

ProLanGO: Protein Function Prediction Using Neural~Machine Translation Based on a Recurrent Neural Network

no code implementations19 Oct 2017 Renzhi Cao, Colton Freitas, Leong Chan, Miao Sun, Haiqing Jiang, Zhangxin Chen

With the development of next generation sequencing techniques, it is fast and cheap to determine protein sequences but relatively slow and expensive to extract useful information from protein sequences because of limitations of traditional biological experimental techniques.

Machine Translation Protein Function Prediction +1

DeepQA: Improving the estimation of single protein model quality with deep belief networks

no code implementations15 Jul 2016 Renzhi Cao, Debswapna Bhattacharya, Jie Hou, Jianlin Cheng

The deep belief network is trained on several large datasets consisting of models from the Critical Assessment of Protein Structure Prediction (CASP) experiments, several publicly available datasets, and models generated by our in-house ab initio method.

Protein Structure Prediction

Evaluation of Protein Structural Models Using Random Forests

no code implementations13 Feb 2016 Renzhi Cao, Taeho Jo, Jianlin Cheng

Our method uses both multi and single model quality assessment method for global quality assessment, and uses chemical, physical, geo-metrical features, and global quality score for local quality assessment.

Protein Structure Prediction

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

1 code implementation3 Jan 2016 Yuxiang Jiang, Tal Ronnen Oron, Wyatt T Clark, Asma R Bankapur, Daniel D'Andrea, Rosalba Lepore, Christopher S Funk, Indika Kahanda, Karin M Verspoor, Asa Ben-Hur, Emily Koo, Duncan Penfold-Brown, Dennis Shasha, Noah Youngs, Richard Bonneau, Alexandra Lin, Sayed ME Sahraeian, Pier Luigi Martelli, Giuseppe Profiti, Rita Casadio, Renzhi Cao, Zhaolong Zhong, Jianlin Cheng, Adrian Altenhoff, Nives Skunca, Christophe Dessimoz, Tunca Dogan, Kai Hakala, Suwisa Kaewphan, Farrokh Mehryary, Tapio Salakoski, Filip Ginter, Hai Fang, Ben Smithers, Matt Oates, Julian Gough, Petri Törönen, Patrik Koskinen, Liisa Holm, Ching-Tai Chen, Wen-Lian Hsu, Kevin Bryson, Domenico Cozzetto, Federico Minneci, David T Jones, Samuel Chapman, Dukka B K. C., Ishita K Khan, Daisuke Kihara, Dan Ofer, Nadav Rappoport, Amos Stern, Elena Cibrian-Uhalte, Paul Denny, Rebecca E Foulger, Reija Hieta, Duncan Legge, Ruth C Lovering, Michele Magrane, Anna N Melidoni, Prudence Mutowo-Meullenet, Klemens Pichler, Aleksandra Shypitsyna, Biao Li, Pooya Zakeri, Sarah ElShal, Léon-Charles Tranchevent, Sayoni Das, Natalie L Dawson, David Lee, Jonathan G Lees, Ian Sillitoe, Prajwal Bhat, Tamás Nepusz, Alfonso E Romero, Rajkumar Sasidharan, Haixuan Yang, Alberto Paccanaro, Jesse Gillis, Adriana E Sedeño-Cortés, Paul Pavlidis, Shou Feng, Juan M Cejuela, Tatyana Goldberg, Tobias Hamp, Lothar Richter, Asaf Salamov, Toni Gabaldon, Marina Marcet-Houben, Fran Supek, Qingtian Gong, Wei Ning, Yuanpeng Zhou, Weidong Tian, Marco Falda, Paolo Fontana, Enrico Lavezzo, Stefano Toppo, Carlo Ferrari, Manuel Giollo, Damiano Piovesan, Silvio Tosatto, Angela del Pozo, José M Fernández, Paolo Maietta, Alfonso Valencia, Michael L Tress, Alfredo Benso, Stefano Di Carlo, Gianfranco Politano, Alessandro Savino, Hafeez Ur Rehman, Matteo Re, Marco Mesiti, Giorgio Valentini, Joachim W Bargsten, Aalt DJ van Dijk, Branislava Gemovic, Sanja Glisic, Vladmir Perovic, Veljko Veljkovic, Nevena Veljkovic, Danillo C Almeida-e-Silva, Ricardo ZN Vencio, Malvika Sharan, Jörg Vogel, Lakesh Kansakar, Shanshan Zhang, Slobodan Vucetic, Zheng Wang, Michael JE Sternberg, Mark N Wass, Rachael P Huntley, Maria J Martin, Claire O'Donovan, Peter N. Robinson, Yves Moreau, Anna Tramontano, Patricia C Babbitt, Steven E Brenner, Michal Linial, Christine A Orengo, Burkhard Rost, Casey S Greene, Sean D Mooney, Iddo Friedberg, Predrag Radivojac

To review progress in the field, the analysis also compared the best methods participating in CAFA1 to those of CAFA2.

Quantitative Methods

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