Thomas Litfin

17 papers Journal 17
YearRankTypeTitle / Venue / Authors
2025 J jnl
Benchmarking the methods for predicting base pairs in RNA-RNA interactions.
Bioinform.
Mei Lang, Thomas Litfin, Ke Chen, Jian Zhan, Yaoqi Zhou
2024 J jnl
MARS and RNAcmap3: The Master Database of All Possible RNA Sequences Integrated with RNAcmap for RNA Homology Search.
Genom. Proteom. Bioinform.
Ke Chen, Thomas Litfin, Jaswinder Singh, Jian Zhan, Yaoqi Zhou
2023 J jnl
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins.
Nucleic Acids Res.
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, Yi Jun Tang, Bin Liu, Claudio Mirabello, Björn Wallner, Burkhard Rost, Dagmar Ilzhöfer, Maria Littmann, Michael Heinzinger, Lea I M. Krautheimer, Michael Bernhofer, Liam J. McGuffin, Isabelle Callebaut, Tristan Bitard Feildel, Jian Liu, Jianlin Cheng, Zhiye Guo, Jinbo Xu, Sheng Wang, Nawar Malhis, Jörg Gsponer, Chol-Song Kim, Kun-Sop Han, Myong-Chol Ma, Lukasz A. Kurgan, Sina Ghadermarzi, Akila Katuwawala, Bi Zhao, Zhenling Peng, Zhonghua Wu, Gang Hu, Kui Wang, Md. Tamjidul Hoque, Md Wasi Ul Kabir, Michele Vendruscolo, Pietro Sormanni, Min Li, Fuhao Zhang, Pengzhen Jia, Yida Wang, Michail Yu. Lobanov, Oxana V. Galzitskaya, Wim F. Vranken, Adrián Díaz, Thomas Litfin, Yaoqi Zhou, Jack Hanson, Kuldip K. Paliwal, Zsuzsanna Dosztányi, Gábor Erdös, Silvio C. E. Tosatto, Damiano Piovesan
2022 J jnl
Predicting RNA distance-based contact maps by integrated deep learning on physics-inferred secondary structure and evolutionary-derived mutational coupling.
Bioinform.
Jaswinder Singh, Kuldip K. Paliwal, Thomas Litfin, Jaspreet Singh, Yaoqi Zhou
2022 J jnl
Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives.
Briefings Bioinform.
Md. Solayman, Thomas Litfin, Jaswinder Singh, Kuldip K. Paliwal, Yaoqi Zhou, Jian Zhan
2022 J jnl
SPOT-Contact-LM: improving single-sequence-based prediction of protein contact map using a transformer language model.
Bioinform.
Jaspreet Singh, Thomas Litfin, Jaswinder Singh, Kuldip K. Paliwal, Yaoqi Zhou
2021 J jnl
Improved RNA secondary structure and tertiary base-pairing prediction using evolutionary profile, mutational coupling and two-dimensional transfer learning.
Bioinform.
Jaswinder Singh, Kuldip K. Paliwal, Tongchuan Zhang, Jaspreet Singh, Thomas Litfin, Yaoqi Zhou
2021 J jnl
RNAcmap: a fully automatic pipeline for predicting contact maps of RNAs by evolutionary coupling analysis.
Bioinform.
Tongchuan Zhang, Jaswinder Singh, Thomas Litfin, Jian Zhan, Kuldip K. Paliwal, Yaoqi Zhou
2021 J jnl
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.
Bioinform.
Jaspreet Singh, Thomas Litfin, Kuldip K. Paliwal, Jaswinder Singh, Anil Kumar Hanumanthappa, Yaoqi Zhou
2020 J jnl
Getting to Know Your Neighbor: Protein Structure Prediction Comes of Age with Contextual Machine Learning.
J. Comput. Biol.
Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou
2020 J jnl
Identifying molecular recognition features in intrinsically disordered regions of proteins by transfer learning.
Bioinform.
Jack Hanson, Thomas Litfin, Kuldip K. Paliwal, Yaoqi Zhou
2020 J jnl
SPOT-Fold: Fragment-Free Protein Structure Prediction Guided by Predicted Backbone Structure and Contact Map.
J. Comput. Chem.
Yufeng Cai, Xiongjun Li, Zhe Sun, Yutong Lu, Huiying Zhao, Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yaoqi Zhou, Yuedong Yang
2019 J jnl
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.
Bioinform.
Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou
2019 J jnl
SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning.
Genom. Proteom. Bioinform.
Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yaoqi Zhou
2019 J jnl
SPOT-Peptide: Template-Based Prediction of Peptide-Binding Proteins and Peptide-Binding Sites.
J. Chem. Inf. Model.
Thomas Litfin, Yuedong Yang, Yaoqi Zhou
2018 J jnl
Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networks.
Bioinform.
Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou
2017 J jnl
SPOT-ligand 2: improving structure-based virtual screening by binding-homology search on an expanded structural template library.
Bioinform.
Thomas Litfin, Yaoqi Zhou, Yuedong Yang