SPOT-ligand 2: improving structure-based virtual screening by binding-homology search on an expanded structural template library. - Thomas Litfin; Yaoqi Zhou; Yuedong Yang (Bioinform., 2017)

Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networks. - Jack Hanson; Kuldip K. Paliwal; Thomas Litfin; Yuedong Yang; Yaoqi Zhou (Bioinform., 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 networks. - Jack Hanson; Kuldip K. Paliwal; Thomas Litfin; Yuedong Yang; Yaoqi Zhou (Bioinform., 2019)

SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning. - Jack Hanson; Kuldip K. Paliwal; Thomas Litfin; Yaoqi Zhou (Genom. Proteom. Bioinform., 2019)

SPOT-Peptide: Template-Based Prediction of Peptide-Binding Proteins and Peptide-Binding Sites. - Thomas Litfin; Yuedong Yang; Yaoqi Zhou (J. Chem. Inf. Model., 2019)

Identifying molecular recognition features in intrinsically disordered regions of proteins by transfer learning. - Jack Hanson; Thomas Litfin; Kuldip K. Paliwal; Yaoqi Zhou (Bioinform., 2020)

Getting to Know Your Neighbor: Protein Structure Prediction Comes of Age with Contextual Machine Learning. - Jack Hanson; Kuldip K. Paliwal; Thomas Litfin; Yuedong Yang; Yaoqi Zhou (J. Comput. Biol., 2020)

SPOT-Fold: Fragment-Free Protein Structure Prediction Guided by Predicted Backbone Structure and Contact Map. - Yufeng Cai; Xiongjun Li; Zhe Sun; Yutong Lu; Huiying Zhao; Jack Hanson; Kuldip K. Paliwal; Thomas Litfin; Yaoqi Zhou; Yuedong Yang (J. Comput. Chem., 2020)

SPOT-1D-Single: improving the single-sequence-based prediction of protein secondary structure, backbone angles, solvent accessibility and half-sphere exposures using a large training set and ensembled deep learning. - Jaspreet Singh; Thomas Litfin; Kuldip K. Paliwal; Jaswinder Singh; Anil Kumar Hanumanthappa; Yaoqi Zhou (Bioinform., 2021)

Improved RNA secondary structure and tertiary base-pairing prediction using evolutionary profile, mutational coupling and two-dimensional transfer learning. - Jaswinder Singh; Kuldip K. Paliwal; Tongchuan Zhang; Jaspreet Singh; Thomas Litfin; Yaoqi Zhou (Bioinform., 2021)

RNAcmap: a fully automatic pipeline for predicting contact maps of RNAs by evolutionary coupling analysis. - Tongchuan Zhang; Jaswinder Singh; Thomas Litfin; Jian Zhan; Kuldip K. Paliwal; Yaoqi Zhou (Bioinform., 2021)

Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives. - Md. Solayman; Thomas Litfin; Jaswinder Singh; Kuldip K. Paliwal; Yaoqi Zhou; Jian Zhan (Briefings Bioinform., 2022)

SPOT-Contact-LM: improving single-sequence-based prediction of protein contact map using a transformer language model. - Jaspreet Singh; Thomas Litfin; Jaswinder Singh; Kuldip K. Paliwal; Yaoqi Zhou (Bioinform., 2022)

Predicting RNA distance-based contact maps by integrated deep learning on physics-inferred secondary structure and evolutionary-derived mutational coupling. - Jaswinder Singh; Kuldip K. Paliwal; Thomas Litfin; Jaspreet Singh; Yaoqi Zhou (Bioinform., 2022)

CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins. - Alessio Del Conte; Adel Bouhraoua; Mahta Mehdiabadi; Damiano Clementel; Alexander Miguel Monzon; Alex S. Holehouse; Daniel A. Griffith; Ryan J. Emenecker; Ashwini Patil; Ronesh Sharma; Tatsuhiko Tsunoda; Alok Sharma; et al. (Nucleic Acids Res., 2023)

MARS and RNAcmap3: The Master Database of All Possible RNA Sequences Integrated with RNAcmap for RNA Homology Search. - Ke Chen; Thomas Litfin; Jaswinder Singh; Jian Zhan; Yaoqi Zhou (Genom. Proteom. Bioinform., 2024)