Side-chain modeling with an optimized scoring function

Por Liang, Shide, Grishin, Nick V.
Publicado em 2002

Refining near-native protein–protein docking decoys by local resampling and energy minimization

Por Liang, Shide, Wang, Guangce, Zhou, Yaoqi
Publicado em 2009

LEAP: Highly accurate prediction of protein loop conformations by integrating coarse-grained sampling and optimized energy scores with all-atom refinement of backbone and side chai...

Por Liang, Shide, Zhang, Chi, Zhou, Yaoqi
Publicado em 2013

Protein binding site prediction using an empirical scoring function

Por Liang, Shide, Zhang, Chi, Liu, Song, Zhou, Yaoqi
Publicado em 2006

A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys

Por Liang, Shide, Liu, Song, Zhang, Chi, Zhou, Yaoqi
Publicado em 2007

Prediction of antigenic epitopes on protein surfaces by consensus scoring

Por Liang, Shide, Zheng, Dandan, Zhang, Chi, Zacharias, Martin
Publicado em 2009

SVMTriP: A Method to Predict Antigenic Epitopes Using Support Vector Machine to Integrate Tri-Peptide Similarity and Propensity

Por Yao, Bo, Zhang, Lin, Liang, Shide, Zhang, Chi
Publicado em 2012

Conformational B-Cell Epitope Prediction on Antigen Protein Structures: A Review of Current Algorithms and Comparison with Common Binding Site Prediction Methods

Por Yao, Bo, Zheng, Dandan, Liang, Shide, Zhang, Chi
Publicado em 2013

Protein Side Chain Modeling with Orientation Dependent Atomic Force Fields Derived by Series Expansions

Por Liang, Shide, Zhou, Yaoqi, Grishin, Nick, Standley, Daron M.
Publicado em 2011

Fast and accurate prediction of protein side-chain conformations

Por Liang, Shide, Zheng, Dandan, Zhang, Chi, Standley, Daron M.
Publicado em 2011

Consensus scoring for enriching near-native structures from protein-protein docking decoys

Por Liang, Shide, Meroueh, Samy O., Wang, Guangce, Qiu, Chao, Zhou, Yaoqi
Publicado em 2009

A novel function prediction approach using protein overlap networks

Por Liang, Shide, Zheng, Dandan, Standley, Daron M, Guo, Huarong, Zhang, Chi
Publicado em 2013

EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results

Por Liang, Shide, Zheng, Dandan, Standley, Daron M, Yao, Bo, Zacharias, Martin, Zhang, Chi
Publicado em 2010

Exploring the Molecular Design of Protein Interaction Sites with Molecular Dynamics Simulations and Free Energy Calculations

Por Liang, Shide, Li, Liwei, Hsu, Wei-Lun, Pilcher, Meaghan N., Uversky, Vladimir, Zhou, Yaoqi, Dunker, A. Keith, Meroueh, Samy O.
Publicado em 2009

Community-wide Evaluation of Methods for Predicting the Effect of Mutations on Protein-Protein Interactions

Por Moretti, Rocco, Fleishman, Sarel J., Agius, Rudi, Torchala, Mieczyslaw, Bates, Paul A., Kastritis, Panagiotis L., Rodrigues, João P. G. L. M., Trellet, Mikaël, Bonvin, Alexandre M. J. J., Cui, Meng, Rooman, Marianne, Gillis, Dimitri, Dehouck, Yves, Moal, Iain, Romero-Durana, Miguel, Perez-Cano, Laura, Pallara, Chiara, Jimenez, Brian, Fernandez-Recio, Juan, Flores, Samuel, Pacella, Michael, Kilambi, Krishna Praneeth, Gray, Jeffrey J., Popov, Petr, Grudinin, Sergei, Esquivel-Rodríguez, Juan, Kihara, Daisuke, Zhao, Nan, Korkin, Dmitry, Zhu, Xiaolei, Demerdash, Omar N. A., Mitchell, Julie C., Kanamori, Eiji, Tsuchiya, Yuko, Nakamura, Haruki, Lee, Hasup, Park, Hahnbeom, Seok, Chaok, Sarmiento, Jamica, Liang, Shide, Teraguchi, Shusuke, Standley, Daron M., Shimoyama, Hiromitsu, Terashi, Genki, Takeda-Shitaka, Mayuko, Iwadate, Mitsuo, Umeyama, Hideaki, Beglov, Dmitri, Hall, David R., Kozakov, Dima, Vajda, Sandor, Pierce, Brian G., Hwang, Howook, Vreven, Thom, Weng, Zhiping, Huang, Yangyu, Li, Haotian, Yang, Xiufeng, Ji, Xiaofeng, Liu, Shiyong, Xiao, Yi, Zacharias, Martin, Qin, Sanbo, Zhou, Huan-Xiang, Huang, Sheng-You, Zou, Xiaoqin, Velankar, Sameer, Janin, Joël, Wodak, Shoshana J., Baker, David
Publicado em 2013