End-to-End Differentiable Learning of Protein Structure

AlQuraishi, Mohammed·2019·Cell Systems
DOI 10.1016/j.cels.2019.03.006

Cited by (374)

Items 301–374 of 374

  1. The role of protein embeddings for protein–protein interaction prediction with graph neural networks
    Laura Balbi, Rita T. Sousa, Pedro Giesteira Cotovio, Cátia Pesquita · 2026 · Briefings in Bioinformatics
  2. Signalkaskaden durch Messen der kodierten Information besser verstehen
    Thomas Dandekar, Meik Kunz · 2017 · Springer eBooks
  3. Structural diversity in the Mycobacteria DUF3349 superfamily
    Garry W. Buchko, Jan A. Abendroth, John Isaac Robinson, Isabelle Q. Phan, Peter John Myler, Thomas E. Edwards · 2019 · Protein Science
  4. Bingham deep neural and oppositional fish swarm optimized protein structure prediction
    Varanavasi Nallasamy, Malarvizhi S. · 2021 · Journal of Biomolecular Structure and Dynamics
  5. Towards Protein Tertiary Structure Prediction Using LSTM/BLSTM
    Jisna Vellara Antony, Akhil Penikalapati, Jaiwanth Reddy, P. N. Pournami, P. B. Jayaraj · 2021 · Lecture notes in electrical engineering
  6. A Progress on Protein Structure Prediction using Various Soft Computing Techniques
    Niharika Chaudhary, Sanjay Saini · 2022 · Computer Science and Information Technology Trends
  7. Artificial Intelligence-Assisted Production of Biomolecules
    Ab Waheed Wani, Atul Baliram Khalangre, Rajni Rajan, Anis Ahmad Mirza, Iftisam Yaseen, Ghlomareza Abdi, Adil Rahim, Maryam Abbasi Tarighat, Krishnananda Pralhad Ingle · 2023 · Springer eBooks
  8. Progress and Research Trends of Artificial Intelligence Incorporation in Protein Structure Prediction
    Maggie Lau · 2024 · IEEE International Conference on Computing and Machine Intelligence (ICMI)
  9. A Review of Protein Structure Prediction using Deep Learning
    Meredita Susanty, Tati Latifah Erawati Rajab, Rukman Hertadi · 2021 · BIO Web of Conferences
  10. Signalkaskaden durch Messen der kodierten Information besser verstehen
    Thomas Dandekar, Meik Kunz · 2021 · Springer eBooks
  11. Epigenetics
    Thomas Edmund Dickins · 2021 · Evolutionary Biology/Evolutionary biology
  12. PENSAMIENTO CRÍTICO EN LA INVESTIGACIÓN CIENTÍFICA Y ACADÉMICA
    Camilo Mauricio Grillo Torres, Jordan Piero Borda Colque, Juan Reynaldo Paredes-Quispe, Jordan Piero Borda Colque, Jordan Piero Borda Colque, Hugo Ticona Salluca, Wilber Pastor, Juan Carlos Buendía Pastrana, José Antonio Ogosi Auqui, José Antonio et al. · 2023
  13. Discovering loop conformational flexibility in T4 lysozyme mutants through artificial intelligence aided molecular dynamics
    Zachary Smith, Pavan Ravindra, Yihang Wang, Rory Cooley, Pratyush Tiwary · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  14. DeepPSC (protein structure camera): computer vision-based protein backbone structure reconstruction from alpha carbon trace as a case study
    Xing Zhang, Junwen Luo, Yi Cai, Wei Zhu, Xiaofeng Yang, Hongmin Cai, Zhanglin Lin · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  15. SidechainNet: An All-Atom Protein Structure Dataset for Machine Learning
    King, Jonathan E., David Ryan Koes · 2020 · arXiv (Cornell University)
  16. Deep Multi-attribute Graph Representation Learning on Protein Structures
    Xia, Tian, Wei‐Shinn Ku · 2020 · arXiv (Cornell University)
  17. AbstractDifferentiation.jl: Backend-Agnostic Differentiable Programming in Julia
    Frank Schäfer, Mohamed Tarek, Lyndon White, Christopher Rackauckas · 2021 · arXiv (Cornell University)
  18. Statistical methods for biological sequence analysis for DNA binding motifs and protein contacts
    Roth, Christian · 2021 · eDiss (Georg-August-Universität Göttingen)
  19. Drug design and repurposing with a sequence-to-drug paradigm
    Lifan Chen, Zisheng Fan, Jie Chang, Ruirui Yang, Hao Guo, Yinghui Zhang, Tianbiao Yang, Chenmao Zhou, Zhengyang Chen, Chen Zheng et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  20. Synthetic Biology
    Aparna B. Murukan, Ayisha A. Jabbar, Akshay Ramesh, Anu Rohit Melge, Nidheesh Melethadathil, Prashanth Suravajhala, Renuka Suravajhala · 2024 · Elsevier eBooks
  21. Connecting the dots: deep learning-based automated model building methods in cryo-EM
    Bansia, Harsh, des Georges, Amedee · 2026 · Frontiers in Molecular Biosciences
  22. Extending genome-scale de novo protein modelling coverage using iterative deep learning-based prediction of structural constraints
    Joe G. Greener, Shaun M. Kandathil, David T. Jones · 2018 · arXiv (Cornell University)
  23. Refinement of protein structure via contact based potentials in replica exchange simulations
    Arthur Voronin, Marie Weiel, Alexander H. Schug · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  24. Decision letter: Bioengineering horizon scan 2020
    2020 · eLife
  25. A systematic structural comparison of all solved small proteins (4-6 kDa) reveals the weight of disulfide bonds in proteins’ foldability
    Mariana H. Moreira, Fábio C. L. Almeida, Tatiana Domitrovic, Fernando Lucas Palhano · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  26. Machine-Learned Molecular Surface and Its Application to Implicit Solvent Simulation
    Haixin Wei, Zekai Zhao, Ray Luo · 2021 · arXiv (Cornell University)
  27. Rapid protein model refinement by deep learning
    Osama Abdin, Philip M. Kim · 2021 · Nature Computational Science
  28. Guardians of the Cell: State-of-the-Art of Membrane Proteins from a Computational Point-of-View
    Nícia Rosário‐Ferreira, Catarina Marques-Pereira, Raquel P. Gouveia, Joana Mourão, Irina Sousa Moreira · 2021 · Methods in molecular biology
  29. Development and Application of Computational Models for Peptide-Protein Complexes
    Isak Johansson-Åkhe · 2022 · Linköping studies in science and technology. Dissertations
  30. The Role of Big Data Analytics in Drug Discovery and Vaccine Development Against COVID-19
    2022 · Advances in data mining and database management book series
  31. Faculty Opinions recommendation of Highly accurate protein structure prediction with AlphaFold.
    Arockia Jeyaprakash Arulanandam · 2021 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  32. Faculty Opinions recommendation of Highly accurate protein structure prediction with AlphaFold.
    Sutirtha Chakraborty · 2021 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  33. ZeroFold-Understanding Mutations of SARS-CoV-2 Spike Protein base on Secondary Structure Event Extracting for guiding Vaccine development
    Weibin Chen, Zhiyuan Xu · 2020
  34. Protein Structure Prediction with Expectation Reflection
    Evan Cresswell-Clay, Danh-Tai Hoang, Joe McKenna, Chris Yang, Eric Zhang, Vipul Periwal · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  35. PRRGNVis: Multi-Level Visual Analysis of Comparison for Predicted Results of Recurrent Geometric Network
    Yanfen Wang, Li Feng, Quan Wang, Yang Xu, Dongliang Guo · 2022 · Applied Sciences
  36. Computer Science and Information Technology Trends
    2022
  37. Linking research of biomedical datasets
    Xiu-Ju George Zhao, Hui Cao · 2022 · Briefings in Bioinformatics
  38. Visualization and Analysis of RecurrentGeometric Network oriented to Protein 3DStructure Prediction
    Kang Ye, Ruibo Gao · 2022 · Research Square
  39. Intelligent Drug Design and Use for Cancer Treatment: The Roles of AI and Precision Oncology in Targeting Patient-Specific Splicing Profiles
    Rodney Hull, Mosebo A. Manabile, Zodwa Dlamini · 2023 · Springer eBooks
  40. How to Better Understand Signal Cascades and Measure the Encoded Information
    Thomas Dandekar, Meik Kunz · 2023 · Springer eBooks
  41. Investigation of Solid Formation Enthalpy and Molecular Mechanics Energies of Amino Acids via Force Field Approach
    Levent SONGUR, Oğuzhan Orhan, S. Özgen · 2023 · Bitlis Eren Üniversitesi Fen Bilimleri Dergisi
  42. Avoiding Machine Learning Becoming Pseudoscience in Biomedical Research
    Meredita Susanty, Ira Puspasari, Nilam Fitriah, Dimitri Mahayana, Tati Latifah Erawati Rajab, Hasballah Zakaria, Agung Wahyu Setiawan, Rukman Hertadi · 2023 · Jurnal Informatika
  43. Automated Protein Affinity Optimization using a 1D-CNN Deep Learning Model
    J. Liam McWhirter, Abhishek Mukhopadhyay, Patrick J. Farber, Greg Lakatos, Surjit B. Dixit · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  44. A Comprehensive Review of the Works of Literature for the Prediction of Protein Structure—Perceptions on Traditional and Deep Learning Approaches
    Prabha Singh, Sudhakar Tripathi, Anand Bihari · 2023 · Lecture notes in networks and systems
  45. Role of artificial intelligence in optimization of drug formulation
    Jasu Rajan, Vasu Rajan, Rishabh Sharma, Rajiv Kumar Sharma · 2023 · AIP conference proceedings
  46. A COMPREHENSIVE REVIEW: EXPLORING ARTIFICIAL INTELLIGENCE IN DRUG DISCOVERY AND DEVELOPMENT
    2024 · International Research Journal of Modernization in Engineering Technology and Science
  47. AlphaFold, the successful prediction of three-dimensional protein structures and its impact on structural biology
    2024 · Elsevier eBooks
  48. Clustering Diffusion Model for Improving Protein Structure Prediction Performance
    Wei Zhong, Xudong Zhang, Ning Yu · 2025 · International Conference on Artificial Intelligence and Big Data (ICAIBD)
  49. Learning molecular machines by machine learning
    Rumeysa Hilal Çelik, Haci Aslan Onur Iscil, Ecem Bulut, Saliha Ece Acuner · 2025 · Eurasian Journal of Science Engineering and Technology
  50. AI Data Applications in Drug Design, Development, and Diagnostics: A Comprehensive Approach to Modern Medicine
    Ritika Singh, Prasoon Pandey, Anuj Kumar, Manoj Kumar Mishra · 2025 · Current Bioinformatics
  51. Deep learning in protein structure prediction
    Jiaxiang Wu · 2025 · Elsevier eBooks
  52. Machine Learning‐driven Ab Initio Protein Design
    Jinjin Li, Yanqiang Han · 2025 · Machine Learning in Protein Science
  53. Allosteric Rate Control of Chaos Governs Reaction Rate Kinetics
    Tjeerd V. olde Scheper, Alex Silverthorne, Holly Tonks, Karl Morten · 2025 · IEEE Transactions on Computational Biology and Bioinformatics
  54. Additional file 1 of Fast activation maximization for molecular sequence design
    Johannes Linder, Georg Seelig · 2021 · Figshare
  55. Fourier Helicity Spectra as Quantifiers of Multiscale Chirality
    Sang Won Im, Jessica Ma, Neel Moudgal, Nicholas A. Kotov · 2025 · bioRxiv
  56. Artificial intelligence-based technologies for advancing research and development in the pharmaceutical industry: current developments and challenges
    Vivek P. Chavda, Arya Vyas, Kashvy R. Morakhia, Swayamprakash Patel, Mangesh Kulkarni, Disha Joshi · 2026 · Elsevier eBooks
  57. Machine learning & geospatial approach for analysing the groundwater quality of J&K region, NW Himalaya
    Avtar Singh Jasrotia, Amit Sharma, Mohinder Lal Angurala, Komal Kumar Singh, Upasna Andotra, Rajesh Kumar · 2026 · Evolving Earth
  58. Statistical mechanics of viral-immune co-evolution
    Jacopo Marchi · 2020
  59. Nouvelles approches pour générer des modèles de moyennes résolutions à l'échelle atomique de structures de protéines à l'aide d'un alphabet structural en absence d'homologues proches
    Surbhi Dhingra · 2020 · theses.fr (ABES)
  60. Nouvelle stratégie d'annotation des génomes par l'utilisation d'algorithmes d'intelligence artificielle
    Nicolas Scalzitti · 2021 · theses.fr (ABES)
  61. Identification and modification of amine dehydrogenases by genomic and structural approaches for biocatalytic amine synthesis
    Laurine Ducrot · 2022
  62. Structural prediction of protein assemblies with deep learning
    Hélène Bret · 2023 · theses.fr (ABES)
  63. Machine Learning Methods for Molecular Dynamic Simulations
    Zineb Belkacemi · 2022 · theses.fr (ABES)
  64. Integrating Artificial Intelligence into Neurotherapeutics: A New Frontier in Drug Design and Precision Healthcare
    Sudhir Kumar Sahoo, Bichitrananda Tripathy, Manasi Khadanga · 2026 · Current Bioinformatics
  65. Protein Design Enters the Artificial Intelligence Era: Foundations, Tools, and Emerging Paradigms
    Yanlin Mi, Arpit Shukla, Mark Tangney, Sabin Tabirca, Venkata V. B. Yallapragada · 2026 · Computational and Structural Biotechnology Journal
  66. FCTFold: A Fused CNN-Transformer Framework for Protein Fold Prediction in AMR Pathogens
    Mousumi Banerjee, Anushree Chakraborty, Sandip Paul, Rachana Banerjee, Kausik Basak · 2026 · Lecture notes in networks and systems
  67. From Heuristics to Deep Generative Models: A Critical Review of Protein Sequence Analysis Architectures for Clinical Decision Support Systems (CDSS)
    Faezeh Rahimzadeh, Leyli Mohammad Khanli, Pedram Salehpour, Faegheh Golabi · 2026 · Expert Systems with Applications
  68. Optimized Machine Learning Models for Efficient Protein Classification Using Sequence Composition Features
    Ayeong Shon, Yuna Cho, Emily Jooah Lee, Claire Yuna Lee, Seojun Lee · 2026 · Smart innovation, systems and technologies
  69. Fast and Interpretable Estimation of Amino Acid Residue Surface Accessibility Based on Protein Contact Graph
    Andrey Timofeev, Alexander Bratchikov, Alexander Anufriev · 2026 · Physchem
  70. Computational methods for alternative proteins
    S Vyshnav, Vino Sundararajan, Sajitha Lulu Sudhakaran · 2026 · Advances in protein chemistry and structural biology
  71. Physics-informed deep learning: A new paradigm for macromolecular recognition and rational protein design
    Haobo Xie, Hao Wang, Xiaojun Yao, Jinyan Li, Yi Pan, Aiping Lü, Xiangxiang Zeng, Dongsheng Cao, Xiangzheng Fu · 2026 · The Innovation Drug Discovery
  72. Structural compatibility is not enough: Current challenges in protein-protein interaction prediction
    Arne Elofsson · 2026 · Molecular Cell
  73. Introduction to the principles of protein engineering
    Josephine Fay Sharp, Michael Kofi Nelson, Meruyert Rustembek, Rituparna Samanta, Lawrence A. Stern · 2026 · Elsevier eBooks
  74. FAIRsharing record for: AlphaFold Protein Structure Database
    FAIRsharing Team, Yuhe Liang · 2025 · FAIRsharing.org