SVMTriP: a method to predict antigenic epitopes using support vector machine to integrate tri-peptide similarity and propensity von Yao, Bo, Zhang, Lin, Liang, Shide, Zhang, Chi

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Prediction of immunogenicity for humanized and full human therapeutic antibodies von Liang, Shide, Zhang, Chi

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Conformational B-cell epitope prediction on antigen protein structures: a review of current algorithms and comparison with common binding site prediction methods von Yao, Bo, Zheng, Dandan, Liang, Shide, Zhang, Chi

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Prediction of antigenic epitopes on protein surfaces by consensus scoring von Liang, Shide, Zheng, Dandan, Zhang, Chi, Zacharias, Martin

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EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results von Liang, Shide, Zheng, Dandan, Standley, Daron M, Yao, Bo, Zacharias, Martin, Zhang, Chi

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Kotai Antibody Builder: automated high-resolution structural modeling of antibodies von Yamashita, Kazuo, Ikeda, Kazuyoshi, Amada, Karlou, Liang, Shide, Tsuchiya, Yuko, Nakamura, Haruki, Shirai, Hiroki, Standley, Daron M

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Fast and accurate prediction of protein side-chain conformations von Liang, Shide, Zheng, Dandan, Zhang, Chi, Standley, Daron M.

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High-resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations von Shirai, Hiroki, Ikeda, Kazuyoshi, Yamashita, Kazuo, Tsuchiya, Yuko, Sarmiento, Jamica, Liang, Shide, Morokata, Tatsuaki, Mizuguchi, Kenji, Higo, Junichi, Standley, Daron M., Nakamura, Haruki

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PITHA: A Webtool to Predict Immunogenicity for Humanized and Fully Human Therapeutic Antibodies von Liang, Shide, Zhang, Chi

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A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys von Liang, Shide, Liu, Song, Zhang, Chi, Zhou, Yaoqi

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Consensus scoring for enriching near-native structures from protein-protein docking decoys von Liang, Shide, Meroueh, Samy O., Wang, Guangce, Qiu, Chao, Zhou, Yaoqi

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Ab Initio Prediction of 3‑D Conformations for Protein Long Loops with High Accuracy and Applications to Antibody CDRH3 Modeling von Liang, Shide, Zhang, Chi, Zhu, Mingfu

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Protein loop selection using orientation-dependent force fields derived by parameter optimization von Liang, Shide, Zhang, Chi, Standley, Daron M.

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B-Cell Epitope Predictions Using Computational Methods von Zheng, Dandan, Liang, Shide, Zhang, Chi

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De novo protein design by an energy function based on series expansion in distance and orientation dependence von Liang, Shide, Li, Zhixiu, Zhan, Jian, Zhou, Yaoqi

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SVMTriP: A Method to Predict B-Cell Linear Antigenic Epitopes von Yao, Bo, Zheng, Dandan, Liang, Shide, Zhang, Chi

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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... von Liang, Shide, Zhang, Chi, Zhou, Yaoqi

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Effective scoring function for protein sequence design von Liang, Shide, Grishin, Nick V.

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EPCES and EPSVR: Prediction of B-Cell Antigenic Epitopes on Protein Surfaces with Conformational Information von Liang, Shide, Zheng, Dandan, Yao, Bo, Zhang, Chi

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Fold recognition by concurrent use of solvent accessibility and residue depth von Liu, Song, Zhang, Chi, Liang, Shide, Zhou, Yaoqi

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