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Predicting protein stability changes induced by single-point mutations has been a persistent challenge over the years, attracting immense interest from numerous researchers.
Adp-ribosylation of membrane proteins catalyzed by cholera toxin: basis of the activation of adenylate cyclase
D Michael Gill and Roberta Meren · 1978
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Protein engineering
Kevin M Ulmer · 1983
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Statistical potentials extracted from protein structures: how accurate are they?
Paul D Thomas and Ken A Dill · 1996
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Prediction of the stability of protein mutants based on structural environment-dependent amino acid substitution and propensity tables
Christopher M Topham, N Srinivasan, and Tom L Blundell · 1997
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Expressed protein ligation: a general method for protein engineering
Tom W Muir, Dolan Sondhi, and Philip A Cole · 1998
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Prediction of stability changes upon single-site mutations using database-derived potentials
Dimitri Gilis and Marianne Rooman · 1999
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Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models
Peter A Kollman, Irina Massova, Carolina Reyes, Bernd Kuhn, Shuanghong Huo, Lillian Chong, Matthew Lee, Taisung Lee, Yong Duan, Wei Wang, et al · 2000
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Exhaustive mutagenesis in silico: multicoordinate free energy calculations on proteins and peptides
Jed W Pitera and Peter A Kollman · 2000
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Replisome-mediated dna replication
Stephen J Benkovic, Ann M Valentine, and Frank Salinas · 2001
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Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations
Charles W Carter Jr, Brendan C LeFebvre, Stephen A Cammer, Alexander Tropsha, and Marshall Hall Edgell · 2001
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Rosetta: A computer program for estimating soil hydraulic parameters with hierarchical pedotransfer functions
Marcel G Schaap, Feike J Leij, and Martinus Th Van Genuchten · 2001
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Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations
Raphael Guerois, Jens Erik Nielsen, and Luis Serrano · 2002
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Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations
AJ Bordner and RA Abagyan · 2004
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A neural-network-based method for predicting protein stability changes upon single point mutations
Emidio Capriotti, Piero Fariselli, and Rita Casadio · 2004
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Molecular dynamics and protein function
Martin Karplus and John Kuriyan · 2005
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Tm-align: a protein structure alignment algorithm based on the tm-score
Yang Zhang and Jeffrey Skolnick · 2005
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Prediction of protein stability changes for single-site mutations using support vector machines
Jianlin Cheng, Arlo Randall, and Pierre Baldi · 2006
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Predicted effects of missense mutations on native-state stability account for phenotypic outcome in phenylketonuria, a paradigm of misfolding diseases
Angel L Pey, François Stricher, Luis Serrano, and Aurora Martinez · 2007
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Sequence analysis and rule development of predicting protein stability change upon mutation using decision tree model
Liang-Tsung Huang, M Michael Gromiha, and Shinn-Ying Ho · 2007
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Mechanical stimuli of skeletal muscle: implications on mtor/p70s6k and protein synthesis
Nelo Eidy Zanchi and Antonio Herbert Lancha · 2008
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Stability effects of mutations and protein evolvability
Nobuhiko Tokuriki and Dan S Tawfik · 2009
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Water-transporting proteins
Thomas Zeuthen · 2010
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Introduction to current and future protein therapeutics: a protein engineering perspective
Paul J Carter · 2011
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Popmusic 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality
Yves Dehouck, Jean Marc Kwasigroch, Dimitri Gilis, and Marianne Rooman · 2011
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Nonlinear structured-illumination microscopy with a photoswitchable protein reveals cellular structures at 50-nm resolution
E Hesper Rego, Lin Shao, John J Macklin, Lukman Winoto, Göran A Johansson, Nicholas Kamps-Hughes, Michael W Davidson, and Mats GL Gustafsson · 2012
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Protein engineering handbook
Stefan Lutz and Uwe Theo Bornscheuer · 2012
Cited alongside, same era.
Immune-responsive gene 1 protein links metabolism to immunity by catalyzing itaconic acid production
Alessandro Michelucci, Thekla Cordes, Jenny Ghelfi, Arnaud Pailot, Norbert Reiling, Oliver Goldmann, Tina Binz, André Wegner, Aravind Tallam, Antonio Rausell, et al · 2013
Cited alongside, same era.
Duet: a server for predicting effects of mutations on protein stability using an integrated computational approach
Douglas EV Pires, David B Ascher, and Tom L Blundell · 2014
Cited alongside, same era.
Inps: predicting the impact of non-synonymous variations on protein stability from sequence
Piero Fariselli, Pier Luigi Martelli, Castrense Savojardo, and Rita Casadio · 2015
Cited alongside, same era.
Maestro-multi agent stability prediction upon point mutations
Josef Laimer, Heidi Hofer, Marko Fritz, Stefan Wegenkittl, and Peter Lackner · 2015
Cited alongside, same era.
Saafec-seq: a sequence-based method for predicting the effect of single point mutations on protein thermodynamic stability
Gen Li, Shailesh Kumar Panday, and Emil Alexov · 2021
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Scones: self-consistent neural network for protein stability prediction upon mutation
Yashas BL Samaga, Shampa Raghunathan, and U Deva Priyakumar · 2021
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Highly accurate protein structure prediction with alphafold
John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko, et al · 2021
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Protein language models and structure prediction: Connection and progression, 2022
Bozhen Hu, Jun Xia, Jiangbin Zheng, Cheng Tan, Yufei Huang, Yongjie Xu, and Stan Z. Li · 2022
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Pifold: Toward effective and efficient protein inverse folding
Zhangyang Gao, Cheng Tan, and Stan Z Li · 2022
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Ease-mm: sequence-based prediction of mutation-induced stability changes with feature-based multiple models
Lukas Folkman, Bela Stantic, Abdul Sattar, and Yaoqi Zhou · 2016
Cited alongside, same era.
Inps-md: a web server to predict stability of protein variants from sequence and structure
Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, and Rita Casadio · 2016
Cited alongside, same era.
Junction tree variational autoencoder for molecular graph generation
Wengong Jin, Regina Barzilay, and Tommi Jaakkola · 2018
Cited alongside, same era.
Dynamut: predicting the impact of mutations on protein conformation, flexibility and stability
Carlos HM Rodrigues, Douglas EV Pires, and David B Ascher · 2018
Cited alongside, same era.
Foldx as protein engineering tool: better than random based approaches?
Oliver Buß, Jens Rudat, and Katrin Ochsenreither · 2018
Cited alongside, same era.
Flex ddg: Rosetta ensemble-based estimation of changes in protein–protein binding affinity upon mutation
Kyle A Barlow, Shane ’O Conch’uir, Samuel Thompson, Pooja Suresh, James E Lucas, Markus Heinonen, and Tanja Kortemme · 2018
Cited alongside, same era.
Quantification of biases in predictions of protein stability changes upon mutations
Fabrizio Pucci, Katrien V Bernaerts, Jean Marc Kwasigroch, and Marianne Rooman · 2018
Cited alongside, same era.
Later among the works it cites.
Alphadesign: A graph protein design method and benchmark on alphafolddb
Zhangyang Gao, Cheng Tan, Stan Li, et al · 2022
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Rfold: Towards simple yet effective rna secondary structure prediction
Cheng Tan, Zhangyang Gao, and Stan Z Li · 2022
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E3bind: An end-to-end equivariant network for protein-ligand docking
Yangtian Zhang, Huiyu Cai, Chence Shi, Bozitao Zhong, and Jian Tang · 2022
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Semiretro: Semi-template framework boosts deep retrosynthesis prediction
Zhangyang Gao, Cheng Tan, Lirong Wu, and Stan Z Li · 2022
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A survey on generative diffusion model
Hanqun Cao, Cheng Tan, Zhangyang Gao, Guangyong Chen, Pheng-Ann Heng, and Stan Z Li · 2022
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Prostata: Protein stability assessment using transformers
Dmitriy Umerenkov, Tatiana I Shashkova, Pavel V Strashnov, Fedor Nikolaev, Maria Sindeeva, Nikita V Ivanisenko, and Olga L Kardymon · 2022
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Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset
Corrado Pancotti, Silvia Benevenuta, Giovanni Birolo, Virginia Alberini, Valeria Repetto, Tiziana Sanavia, Emidio Capriotti, and Piero Fariselli · 2022
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Continuous-discrete convolution for geometry-sequence modeling in proteins
Hehe Fan, Zhangyang Wang, Yi Yang, and Mohan Kankanhalli · 2022
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Proteins’ evolution upon point mutations
Jorge A Vila · 2022
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Vqpl: Vector quantized protein language
Zhangyang Gao, Cheng Tan, and Stan Z Li · 2023
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Global-context aware generative protein design
Cheng Tan, Zhangyang Gao, Jun Xia, Bozhen Hu, and Stan Z Li · 2023
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Hierarchical data-efficient representation learning for tertiary structure-based rna design, 2023
Cheng Tan, Yijie Zhang, Zhangyang Gao, Hanqun Cao, and Stan Z. Li · 2023
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Knowledge-design: Pushing the limit of protein deign via knowledge refinement
Zhangyang Gao, Cheng Tan, and Stan Z Li · 2023
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Target-aware molecular graph generation
Cheng Tan, Zhangyang Gao, and Stan Z Li · 2023
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Co-supervised pre-training of pocket and ligand
Zhangyang Gao, Cheng Tan, Jun Xia, and Stan Z Li · 2023
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Cross-gate mlp with protein complex invariant embedding is a one-shot antibody designer
Cheng Tan, Zhangyang Gao, and Stan Z Li · 2023
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Zhangyang Gao, Xingran Chen, Cheng Tan, and Stan Z Li · 2023
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Stability oracle: A structure-based graph-transformer for identifying stabilizing mutations
Daniel J Diaz, Chengyue Gong, Jeffrey Ouyang-Zhang, James M Loy, Jordan Wells, David Yang, Andrew D Ellington, Alex Dimakis, and Adam R Klivans · 2023
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Pros-gnn: Predicting effects of mutations on protein stability using graph neural networks
Shuyu Wang, Hongzhou Tang, Peng Shan, Zhaoxia Wu, and Lei Zuo · 2023
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