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Bioinformatics (Oxford, England)|January 7, 2017
SPOT-ligand 2: improving structure-based virtual screening by binding-homology search on an expanded structural template libraryThomas Litfin, Yaoqi Zhou, Yuedong YangJournal of Chemical Information and Modeling|January 31, 2019
SPOT-Peptide: Template-Based Prediction of Peptide-Binding Proteins and Peptide-Binding SitesThomas Litfin, Yuedong Yang, Yaoqi ZhouBioinformatics (Oxford, England)|June 23, 2018
Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networksJack Hanson, Kuldip Paliwal, Thomas Litfin, et al.Bioinformatics (Oxford, England)|December 12, 2018
Improving prediction of protein secondary structure, backbone angles, solvent accessibility and contact numbers by using predicted contact maps and an ensemble of recurrent and residual convolutional neural networksJack Hanson, Kuldip Paliwal, Thomas Litfin, et al.Journal of Computational Biology : a Journal of Computational Molecular Cell Biology|August 8, 2019
Getting to Know Your Neighbor: Protein Structure Prediction Comes of Age with Contextual Machine LearningJack Hanson, Kuldip K Paliwal, Thomas Litfin, et al.Journal of Computational Chemistry|December 24, 2015
Effective protein conformational sampling based on predicted torsion anglesYuedong Yang, Yaoqi ZhouProtein Science : a Publication of the Protein Society|May 13, 2008
Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functionsYuedong Yang, Yaoqi ZhouProteins|February 9, 2008
Specific interactions for ab initio folding of protein terminal regions with secondary structuresYuedong Yang, Yaoqi ZhouBioinformatics (Oxford, England)|September 11, 2019
Identifying molecular recognition features in intrinsically disordered regions of proteins by transfer learningJack Hanson, Thomas Litfin, Kuldip Paliwal, et al.RNA Biology|November 12, 2022
High-throughput mapping of RNA solvent accessibility at the single-nucleotide resolution by RtcB ligation between a fixed 5'-OH-end linker and unique 3'-P-end fragments from hydroxyl radical cleavageMd Solayman, Thomas Litfin, Yaoqi Zhou, et al.Pageof 38