
BioMed Research International 2020 (apr 2020), 1-12. Protein Contact Map Prediction Based on ResNet and DenseNet. Zhong Li, Yuele Lin, Arne Elofsson, and Yuhua Yao.In 4th International Conference on Learning Representations, ICLR 2016, San Juan, Puerto Rico, May 2-4, 2016, Conference Track Proceedings, Yoshua Bengio and Yann LeCun (Eds.). Yujia Li, Daniel Tarlow, Marc Brockschmidt, and Richard S.In 2019 IEEE/CVF International Conference on Computer Vision, ICCV 2019, Seoul, Korea (South), October 27 - November 2, 2019.
Critical assessment of methods of protein structure prediction (CASP)-Round XIII.
Andriy Kryshtafovych, Torsten Schwede, Maya Topf, Krzysztof Fidelis, and John Moult. In 8th International Conference on Learning Representations, ICLR 2020, Addis Ababa, Ethiopia, April 26-30, 2020. Directional Message Passing for Molecular Graphs. Johannes Klicpera, Janek Groß, and Stephan Günnemann. In 3rd International Conference on Learning Representations, ICLR 2015, San Diego, CA, USA, May 7-9, 2015, Conference Track Proceedings, Yoshua Bengio and Yann LeCun (Eds.). Adam: A Method for Stochastic Optimization. Structure-Based Function Prediction using Graph Convolutional Networks. Douglas Renfrew, Tomasz Kosciolek, Julia Koehler Leman, Kyunghyun Cho, Tommi Vatanen, Daniel Berenberg, Bryn Taylor, Ian M. RaptorX-Angle: real-value prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning. Yujuan Gao, Sheng Wang, Minghua Deng, and Jinbo Xu. Deep Neural Network for Protein Contact Prediction by Weighting Sequences in a Multiple Sequence Alignment. IG-VAE: Generative Modeling of Immunoglobulin Proteins by Direct 3D Coordinate Generation. Energy-based models for atomic-resolution protein conformations. Yilun Du, Joshua Meier, Jerry Ma, Rob Fergus, and Alexander Rives. Three-Dimensionally Embedded Graph Convolutional Network (3DGCN) for Molecule Interpretation. PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta. Sidhartha Chaudhury, Sergey Lyskov, and Jeffrey J Gray. ProSPr: Democratized Implementation of Alphafold Protein Distance Prediction Network. Wendy M Billings, Bryce Hedelius, Todd Millecam, David Wingate, and Dennis Della Corte. Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes. J J K 3D GRAPH SOFTWARE
Fast index based algorithms and software for matching position specific scoring matrices.
Michael Beckstette, Robert Homann, Robert Giegerich, and Stefan Kurtz.Deep Generative Models for Highly Structured Data, 2019 Workshop 11 (2019), 1-10. Fully differentiable full-atom protein backbone generation. Namrata Anand, Raphael Eguchi, and Po Ssu Huang.End-to-End Differentiable Learning of Protein Structure. DEEPCON: protein contact prediction using dilated convolutional neural networks with dropout.