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Author Details

Shide Liang
1999
34
17
PMIDPaper TitleJournal TitlePublished Year
38018130Ab Initio Prediction of 3-D Conformations for Protein Long Loops with High Accuracy and Applications to Antibody CDRH3 Modeling.2023
36346595B-Cell Epitope Predictions Using Computational Methods.Methods in Molecular Biology2023
36346590PITHA: A Webtool to Predict Immunogenicity for Humanized and Fully Human Therapeutic Antibodies.Methods in Molecular Biology2023
34406339De novo protein design by an energy function based on series expansion in distance and orientation dependence.2021
32866159Prediction of immunogenicity for humanized and full human therapeutic antibodies.PLoS ONE2020
32162263SVMTriP: A Method to Predict B-Cell Linear Antigenic Epitopes.Methods in Molecular Biology2020
32162262EPCES and EPSVR: Prediction of B-Cell Antigenic Epitopes on Protein Surfaces with Conformational Information.Methods in Molecular Biology2020
25064566Kotai Antibody Builder: automated high-resolution structural modeling of antibodies.Bioinformatics2014
24327406LEAP: highly accurate prediction of protein loop conformations by integrating coarse-grained sampling and optimized energy scores with all-atom refinement of backbone and side chains.Journal of Computational Chemistry2014
24756852High-resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations.Proteins2014
23620816Conformational B-cell epitope prediction on antigen protein structures: a review of current algorithms and comparison with common binding site prediction methods.PLoS ONE2013
23866986A novel function prediction approach using protein overlap networks.BMC Syst Biol2013
23843247Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.Proteins2013
22984622SVMTriP: a method to predict antigenic epitopes using support vector machine to integrate tri-peptide similarity and propensity.PLoS ONE2012
26593673Protein Loop Modeling with Optimized Backbone Potential Functions.J Chem Theory Comput2012
21873640Fast and accurate prediction of protein side-chain conformations.Bioinformatics2011
21374632Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions.J Comput Chem2011
21574188Protein loop selection using orientation-dependent force fields derived by parameter optimization.Proteins2011
20637083EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results.BMC Bioinformatics2010
18831053Consensus scoring for enriching near-native structures from protein-protein docking decoys.Proteins: Structure, Function and Bioinformatics2009
19643976Incorporating receptor flexibility in the molecular design of protein interfaces.Protein Engineering, Design and Selection2009
19156819Refining near-native protein-protein docking decoys by local resampling and energy minimization.Proteins: Structure, Function and Bioinformatics2009
19113835Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculations.Biochemistry2009
19772615Prediction of antigenic epitopes on protein surfaces by consensus scoring.BMC Bioinformatics2009
17623864A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys.Proteins: Structure, Function and Bioinformatics2007
17510969Fold recognition by concurrent use of solvent accessibility and residue depth.Proteins: Structure, Function and Bioinformatics2007
16893954Protein binding site prediction using an empirical scoring function.Nucleic Acids Research2006
14696189Effective scoring function for protein sequence design.Proteins: Structure, Function and Bioinformatics2004
15382230Prediction of the interaction site on the surface of an isolated protein structure by analysis of side chain energy scores.Proteins: Structure, Function and Bioinformatics2004
12471599Beyond the rotamer library: genetic algorithm combined with the disturbing mutation process for upbuilding protein side-chains.Proteins: Structure, Function and Bioinformatics2003
11790842Side-chain modeling with an optimized scoring function.Protein Science2002
10984403Construction of protein binding sites in scaffold structures.Biopolymers2000
10798527Grafting of protein-protein interaction epitope.Journal of Biomolecular Structure and Dynamics2000
10611401Exploring the conformational diversity of loops on conserved frameworks.1999
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