@ARTICLE{Figueredo:2009dg,
   author = {Figueredo, A.~J. and Wolf, P. S.~A.},
   title = {Assortative pairing and life history strategy -- a cross-cultural study},
   journal = {Human Nature},
   volume = {20},
   pages = {317-330},
   year = {2009},
   doi={https://doi.org/10.1007/s12110-009-9068-2}
}

@MISC{Hao:gidmaps:2014,
  author = {Hao, Z. and AghaKouchak, A. and Nakhjiri, N. and Farahmand, A},
  year = {2014},
  title = {Global integrated drought monitoring and prediction system ({GIDMaPS}) data sets},
  howpublished = {\emph{figshare} \url{http://dx.doi.org/10.6084/m9.figshare.853801}}
}


@article{hughes2011principles,
  title={Principles of early drug discovery},
  author={Hughes, James P and Rees, Sally and Kalindjian, Stephen B and Philpott, Kevin L},
  journal={British Journal of Pharmacology},
  volume={162},
  number={6},
  pages={1239--1249},
  year={2011},
  publisher={Wiley Online Library}
}

@article{arnold1998design,
  title={Design by directed evolution},
  author={Arnold, Frances H},
  journal={Accounts of Chemical Research},
  volume={31},
  number={3},
  pages={125--131},
  year={1998},
  publisher={ACS Publications}
}


@book{branden2012introduction,
  title={Introduction to protein structure},
  author={Branden, Carl Ivar and Tooze, John},
  year={2012},
  publisher={Garland Science}
}

@article{jumper2021highly,
  title={Highly accurate protein structure prediction with AlphaFold},
  author={Jumper, John and Evans, Richard and Pritzel, Alexander and Green, Tim and Figurnov, Michael and Ronneberger, Olaf and Tunyasuvunakool, Kathryn and Bates, Russ and {\v{Z}}{\'\i}dek, Augustin and Potapenko, Anna and others},
  journal={Nature},
  volume={596},
  number={7873},
  pages={583--589},
  year={2021},
  publisher={Nature Publishing Group}
}

@article{baek2021accurate,
  title={Accurate prediction of protein structures and interactions using a three-track neural network},
  author={Baek, Minkyung and DiMaio, Frank and Anishchenko, Ivan and Dauparas, Justas and Ovchinnikov, Sergey and Lee, Gyu Rie and Wang, Jue and Cong, Qian and Kinch, Lisa N and Schaeffer, R Dustin and others},
  journal={Science},
  volume={373},
  number={6557},
  pages={871--876},
  year={2021},
  publisher={American Association for the Advancement of Science}
}

@book{alberts2015essential,
  title={Essential cell biology},
  author={Alberts, Bruce and Bray, Dennis and Hopkin, Karen and Johnson, Alexander D and Lewis, Julian and Raff, Martin and Roberts, Keith and Walter, Peter},
  year={2015},
  publisher={Garland Science}
}

@article{arnold2001combinatorial,
  title={Combinatorial and computational challenges for biocatalyst design},
  author={Arnold, Frances H},
  journal={Nature},
  volume={409},
  number={6817},
  pages={253--257},
  year={2001},
  publisher={Nature Publishing Group UK London}
}

@article{huang2016coming,
  title={The coming of age of de novo protein design},
  author={Huang, Po-Ssu and Boyken, Scott E and Baker, David},
  journal={Nature},
  volume={537},
  number={7620},
  pages={320--327},
  year={2016},
  publisher={Nature Publishing Group UK London}
}


@article{dill2008protein,
  title={The protein folding problem},
  author={Dill, Ken A and Ozkan, S Banu and Shell, M Scott and Weikl, Thomas R},
  journal={Annu. Rev. Biophys.},
  volume={37},
  number={1},
  pages={289--316},
  year={2008},
  publisher={Annual Reviews}
}

@article{bryant2021deep,
  title={Deep diversification of an AAV capsid protein by machine learning},
  author={Bryant, Drew H and Bashir, Ali and Sinai, Sam and Jain, Nina K and Ogden, Pierce J and Riley, Patrick F and Church, George M and Colwell, Lucy J and Kelsic, Eric D},
  journal={Nature Biotechnology},
  volume={39},
  number={6},
  pages={691--696},
  year={2021},
  publisher={Nature Publishing Group US New York}
}

@article{lee2022proteinsgm,
  title={ProteinSGM: Score-based generative modeling for protein backbone generation},
  author={Lee, Hoang and Yoon, Seokhyun and Kim, Doheon},
  journal={bioRxiv},
  year={2022},
  publisher={Cold Spring Harbor Laboratory}
}


@article{yang2022protein,
  title={ProteinDT: Generative Modeling for Protein Sequence Design Using Text Descriptions},
  author={Yang, Kai and Wu, Zheng and Arnold, Frances H},
  journal={bioRxiv},
  year={2022},
  publisher={Cold Spring Harbor Laboratory}
}

@article{liu2023text,
  title={A text-guided protein design framework},
  author={Liu, Shengchao and Li, Yanjing and Li, Zhuoxinran and Gitter, Anthony and Zhu, Yutao and Lu, Jiarui and Xu, Zhao and Nie, Weili and Ramanathan, Arvind and Xiao, Chaowei and others},
  journal={arXiv preprint arXiv:2302.04611},
  year={2023}
}

@article{dai2024toward,
  title={Toward De Novo Protein Design from Natural Language},
  author={Dai, Fengyuan and Fan, Yuliang and Su, Jin and Wang, Chentong and Han, Chenchen and Zhou, Xibin and Liu, Jianming and Qian, Hui and Wang, Shunzhi and Zeng, Anping and others},
  journal={bioRxiv},
  pages={2024--08},
  year={2024},
  publisher={Cold Spring Harbor Laboratory}
}

@article{lecun2015deep,
  title={Deep learning},
  author={LeCun, Yann and Bengio, Yoshua and Hinton, Geoffrey},
  journal={Nature},
  volume={521},
  number={7553},
  pages={436--444},
  year={2015},
  publisher={Nature Publishing Group}
}

@inproceedings{krizhevsky2012imagenet,
  title={ImageNet classification with deep convolutional neural networks},
  author={Krizhevsky, Alex and Sutskever, Ilya and Hinton, Geoffrey E},
  booktitle={Advances in Neural Information Processing Systems},
  pages={1097--1105},
  year={2012}
}

@inproceedings{vaswani2017attention,
  title={Attention is all you need},
  author={Vaswani, Ashish and Shazeer, Noam and Parmar, Niki and others},
  booktitle={Advances in Neural Information Processing Systems},
  pages={5998--6008},
  year={2017}
}


@article{brown2020language,
  title={Language models are few-shot learners},
  author={Brown, Tom and Mann, Benjamin and Ryder, Nick and Subbiah, Melanie and Kaplan, Jared D and Dhariwal, Prafulla and Neelakantan, Arvind and Shyam, Pranav and Sastry, Girish and Askell, Amanda and others},
  journal={Advances in neural information processing systems},
  volume={33},
  pages={1877--1901},
  year={2020}
}

@article{goodfellow2014generative,
  title={Generative adversarial nets},
  author={Goodfellow, Ian and Pouget-Abadie, Jean and Mirza, Mehdi and Xu, Bing and Warde-Farley, David and Ozair, Sherjil and Courville, Aaron and Bengio, Yoshua},
  journal={Advances in neural information processing systems},
  volume={27},
  year={2014}
}

@article{dhariwal2021diffusion,
  title={Diffusion models beat gans on image synthesis},
  author={Dhariwal, Prafulla and Nichol, Alexander},
  journal={Advances in neural information processing systems},
  volume={34},
  pages={8780--8794},
  year={2021}
}

@inproceedings{sohl2015deep,
  title={Deep unsupervised learning using nonequilibrium thermodynamics},
  author={Sohl-Dickstein, Jascha and Weiss, Eric and Maheswaranathan, Niru and Ganguli, Surya},
  booktitle={International conference on machine learning},
  pages={2256--2265},
  year={2015},
  organization={PMLR}
}

@article{alley2019unified,
  title={Unified rational protein engineering with sequence-based deep representation learning},
  author={Alley, Ethan C and Khimulya, Grigory and Biswas, Surojit and AlQuraishi, Mohammed and Church, George M},
  journal={Nature methods},
  volume={16},
  number={12},
  pages={1315--1322},
  year={2019},
  publisher={Nature Publishing Group US New York}
}

@misc{vicuna2023,
    title = {Vicuna: An Open-Source Chatbot Impressing GPT-4 with 90\%* ChatGPT Quality},
    url = {https://lmsys.org/blog/2023-03-30-vicuna/},
    author = {Chiang, Wei-Lin and Li, Zhuohan and Lin, Zi and Sheng, Ying and Wu, Zhanghao and Zhang, Hao and Zheng, Lianmin and Zhuang, Siyuan and Zhuang, Yonghao and Gonzalez, Joseph E. and Stoica, Ion and Xing, Eric P.},
    month = {March},
    year = {2023}
}


@incollection{leaver2011rosetta3,
  title={ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules},
  author={Leaver-Fay, Andrew and Tyka, Michael and Lewis, Steven M and Lange, Oliver F and Thompson, James and Jacak, Ron and Kaufman, Kristian W and Renfrew, P Douglas and Smith, Colin A and Sheffler, Will and others},
  booktitle={Methods in enzymology},
  volume={487},
  pages={545--574},
  year={2011},
  publisher={Elsevier}
}

@article{karplus2002molecular,
  title={Molecular dynamics simulations of biomolecules},
  author={Karplus, Martin and McCammon, J Andrew},
  journal={Nature structural biology},
  volume={9},
  number={9},
  pages={646--652},
  year={2002},
  publisher={Nature Publishing Group US New York}
}



@article{kopp2004swiss,
  title={The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models},
  author={Kopp, J{\"u}rgen and Schwede, Torsten},
  journal={Nucleic acids research},
  volume={32},
  number={suppl\_1},
  pages={D230--D234},
  year={2004},
  publisher={Oxford University Press}
}

@article{hollingsworth2018molecular,
  title={Molecular dynamics simulation for all},
  author={Hollingsworth, Scott A and Dror, Ron O},
  journal={Neuron},
  volume={99},
  number={6},
  pages={1129--1143},
  year={2018},
  publisher={Elsevier}
}



@article{lavecchia2015machine,
  title={Machine-learning approaches in drug discovery: methods and applications},
  author={Lavecchia, Antonio},
  journal={Drug discovery today},
  volume={20},
  number={3},
  pages={318--331},
  year={2015},
  publisher={Elsevier}
}



@article{tunyasuvunakool2021highly,
  title={Highly accurate protein structure prediction for the human proteome},
  author={Tunyasuvunakool, Kathryn and Adler, Jonas and Wu, Zachary and Green, Tim and Zielinski, Michal and {\v{Z}}{\'\i}dek, Augustin and Bridgland, Alex and Cowie, Andrew and Meyer, Clemens and Laydon, Agata and others},
  journal={Nature},
  volume={596},
  number={7873},
  pages={590--596},
  year={2021},
  publisher={Nature Publishing Group UK London}
}

@article{senior2020improved,
  title={Improved protein structure prediction using potentials from deep learning},
  author={Senior, Andrew W and Evans, Richard and Jumper, John and Kirkpatrick, James and Sifre, Laurent and Green, Tim and Qin, Chongli and {\v{Z}}{\'\i}dek, Augustin and Nelson, Alexander WR and Bridgland, Alex and others},
  journal={Nature},
  volume={577},
  number={7792},
  pages={706--710},
  year={2020},
  publisher={Nature Publishing Group UK London}
}


@article{del2021methodology,
  title={Methodology for rigorous modeling of protein conformational changes by Rosetta using DEER distance restraints},
  author={Del Alamo, Diego and Jagessar, Kevin L and Meiler, Jens and Mchaourab, Hassane S},
  journal={PLoS Computational Biology},
  volume={17},
  number={6},
  pages={e1009107},
  year={2021},
  publisher={Public Library of Science San Francisco, CA USA}
}


@article{repecka2021expanding,
  title={Expanding functional protein sequence spaces using generative adversarial networks},
  author={Repecka, Donatas and Jauniskis, Vykintas and Karpus, Laurynas and Rembeza, Elzbieta and Rokaitis, Irmantas and Zrimec, Jan and Poviloniene, Simona and Laurynenas, Audrius and Viknander, Sandra and Abuajwa, Wissam and others},
  journal={Nature Machine Intelligence},
  volume={3},
  number={4},
  pages={324--333},
  year={2021},
  publisher={Nature Publishing Group UK London}
}

@article{kingma2013auto,
  title={Auto-encoding variational bayes},
  author={Kingma, Diederik P and Welling, Max},
  journal={arXiv preprint arXiv:1312.6114},
  year={2013}
}

@article{riesselman2018deep,
  title={Deep generative models of genetic variation capture the effects of mutations},
  author={Riesselman, Adam J and Ingraham, John B and Marks, Debora S},
  journal={Nature methods},
  volume={15},
  number={10},
  pages={816--822},
  year={2018},
  publisher={Nature Publishing Group US New York}
}



@article{ferruz2022protgpt2,
  title={ProtGPT2 is a deep unsupervised language model for protein design},
  author={Ferruz, Noelia and Schmidt, Steffen and H{\"o}cker, Birte},
  journal={Nature communications},
  volume={13},
  number={1},
  pages={4348},
  year={2022},
  publisher={Nature Publishing Group UK London}
}


@article{cheng2008machine,
  title={Machine learning methods for protein structure prediction},
  author={Cheng, Jianlin and Tegge, Allison N and Baldi, Pierre},
  journal={IEEE reviews in biomedical engineering},
  volume={1},
  pages={41--49},
  year={2008},
  publisher={IEEE}
}

@article{rives2021biological,
  title={Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences},
  author={Rives, Alexander and Meier, Joshua and Sercu, Tom and Goyal, Siddharth and Lin, Zeming and Liu, Jason and Guo, Demi and Ott, Myle and Zitnick, C Lawrence and Ma, Jerry and others},
  journal={Proceedings of the National Academy of Sciences},
  volume={118},
  number={15},
  pages={e2016239118},
  year={2021},
  publisher={National Acad Sciences}
}

@article{brandes2022proteinbert,
  title={ProteinBERT: a universal deep-learning model of protein sequence and function},
  author={Brandes, Nadav and Ofer, Dan and Peleg, Yam and Rappoport, Nadav and Linial, Michal},
  journal={Bioinformatics},
  volume={38},
  number={8},
  pages={2102--2110},
  year={2022},
  publisher={Oxford University Press}
}


@article{ingraham2019generative,
  title={Generative models for graph-based protein design},
  author={Ingraham, John and Garg, Vikas and Barzilay, Regina and Jaakkola, Tommi},
  journal={Advances in neural information processing systems},
  volume={32},
  year={2019}
}

@article{baldassarre2021graphqa,
  title={GraphQA: protein model quality assessment using graph convolutional networks},
  author={Baldassarre, Federico and Men{\'e}ndez Hurtado, David and Elofsson, Arne and Azizpour, Hossein},
  journal={Bioinformatics},
  volume={37},
  number={3},
  pages={360--366},
  year={2021},
  publisher={Oxford University Press}
}

@article{gainza2020deciphering,
  title={Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning},
  author={Gainza, Pablo and Sverrisson, Freyr and Monti, Frederico and Rodola, Emanuele and Boscaini, Davide and Bronstein, Michael M and Correia, Bruno E},
  journal={Nature Methods},
  volume={17},
  number={2},
  pages={184--192},
  year={2020},
  publisher={Nature Publishing Group US New York}
}


@article{berman2000protein,
  title={The protein data bank},
  author={Berman, Helen M and Westbrook, John and Feng, Zukang and Gilliland, Gary and Bhat, Talapady N and Weissig, Helge and Shindyalov, Ilya N and Bourne, Philip E},
  journal={Nucleic acids research},
  volume={28},
  number={1},
  pages={235--242},
  year={2000},
  publisher={Oxford University Press}
}

@article{devlin2018bert,
  title={Bert: Pre-training of deep bidirectional transformers for language understanding},
  author={Devlin, Jacob and Chang, Ming-Wei and Lee, Kenton and Toutanova, Kristina},
  journal={arXiv preprint arXiv:1810.04805},
  year={2018}
}



@article{yang2020improved,
  title={Improved protein structure prediction using predicted interresidue orientations},
  author={Yang, Jianyi and Anishchenko, Ivan and Park, Hahnbeom and Peng, Zhenling and Ovchinnikov, Sergey and Baker, David},
  journal={Proceedings of the National Academy of Sciences},
  volume={117},
  number={3},
  pages={1496--1503},
  year={2020},
  publisher={National Acad Sciences}
}



@inproceedings{ronneberger2015u,
  title={U-net: Convolutional networks for biomedical image segmentation},
  author={Ronneberger, Olaf and Fischer, Philipp and Brox, Thomas},
  booktitle={Medical image computing and computer-assisted intervention--MICCAI 2015: 18th international conference, Munich, Germany, October 5-9, 2015, proceedings, part III 18},
  pages={234--241},
  year={2015},
  organization={Springer}
}


@inproceedings{he2016deep,
  title={Deep residual learning for image recognition},
  author={He, Kaiming and Zhang, Xiangyu and Ren, Shaoqing and Sun, Jian},
  booktitle={Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition},
  pages={770--778},
  year={2016}
}



@article{huang2011rosettaremodel,
  title={RosettaRemodel: A generalized framework for flexible backbone protein design},
  author={Huang, Po-Ssu AND Ban, Yih-En Andrew AND Richter, Florian AND Andre, Ingemar AND Vernon, Robert AND Schief, William R. AND Baker, David},
  journal={PLoS One},
  volume={6},
  number={8},
  pages={e24109},
  year={2011},
  publisher={Public Library of Science}
}

@article{conway2014rosetta,
  title={Relaxation of backbone bond geometry improves protein energy landscape modeling},
  author={Conway, Patrick and Tyka, Michael D. and DiMaio, Frank and Konerding, David E. and Baker, David},
  journal={Protein Science},
  volume={23},
  number={1},
  pages={47--55},
  year={2014},
  publisher={Wiley Online Library}
}


@article{DBLP:journals/corr/abs-2112-10752,
  author       = {Robin Rombach and
                  Andreas Blattmann and
                  Dominik Lorenz and
                  Patrick Esser and
                  Bj{\"{o}}rn Ommer},
  title        = {High-Resolution Image Synthesis with Latent Diffusion Models},
  journal      = {CoRR},
  volume       = {abs/2112.10752},
  year         = {2021},
  url          = {https://arxiv.org/abs/2112.10752},
}

@article{Xu2010HowSI,
  title={How significant is a protein structure similarity with TM-score = 0.5?},
  author={Jinrui Xu and Yang Zhang},
  journal={Bioinformatics},
  year={2010},
  volume={26 7},
  pages={
          889-95
        },
  url={https://api.semanticscholar.org/CorpusID:17691984}
}



@article{Kingma2014AdamAM,
  title={Adam: A Method for Stochastic Optimization},
  author={Diederik P. Kingma and Jimmy Ba},
  journal={CoRR},
  year={2014},
  volume={abs/1412.6980},
  url={https://api.semanticscholar.org/CorpusID:6628106}
}

@inproceedings{ho2020denoising,
  title={Denoising diffusion probabilistic models},
  author={Ho, Jonathan and Jain, Ajay and Abbeel, Pieter},
  booktitle={Advances in Neural Information Processing Systems},
  volume={33},
  pages={6840--6851},
  year={2020}
}


@article{song2021scorebased,
  title={Score-Based Generative Modeling through Stochastic Differential Equations},
  author={Yang Song and Jascha Narain Sohl-Dickstein and Diederik P. Kingma and Abhishek Kumar and Stefano Ermon and Ben Poole},
  journal={ArXiv},
  year={2020},
  volume={abs/2011.13456},
  url={https://api.semanticscholar.org/CorpusID:227209335}
}



