Protein Structure Prediction: Conventional and Deep Learning Perspectives
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Title
Protein Structure Prediction: Conventional and Deep Learning Perspectives
Authors
Keywords
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Journal
PROTEIN JOURNAL
Volume 40, Issue 4, Pages 522-544
Publisher
Springer Science and Business Media LLC
Online
2021-05-29
DOI
10.1007/s10930-021-10003-y
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Related references
Note: Only part of the references are listed.- Improved protein structure prediction using potentials from deep learning
- (2020) Andrew W. Senior et al. NATURE
- FASPR: an open-source tool for fast and accurate protein side-chain packing
- (2020) Xiaoqiang Huang et al. BIOINFORMATICS
- Enhancing fragment-based protein structure prediction by customising fragment cardinality according to local secondary structure
- (2020) Jad Abbass et al. BMC BIOINFORMATICS
- Protein Contact Map Prediction Based on ResNet and DenseNet
- (2020) Zhong Li et al. Biomed Research International
- DeepCDpred: Inter-residue distance and contact prediction for improved prediction of protein structure
- (2019) Shuangxi Ji et al. PLoS One
- Protein tertiary structure modeling driven by deep learning and contact distance prediction in CASP13
- (2019) Jie Hou et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- End-to-End Differentiable Learning of Protein Structure
- (2019) Mohammed AlQuraishi Cell Systems
- DEEPCON: Protein Contact Prediction using Dilated Convolutional Neural Networks with Dropout
- (2019) Badri Adhikari BIOINFORMATICS
- ProteinNet: a standardized data set for machine learning of protein structure
- (2019) Mohammed AlQuraishi BMC BIOINFORMATICS
- OPUS-Rota2: An Improved Fast and Accurate Side-Chain Modeling Method
- (2019) Gang Xu et al. Journal of Chemical Theory and Computation
- Analysis of distance‐based protein structure prediction by deep learning in CASP13
- (2019) Jinbo Xu et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13)
- (2019) Andrew W. Senior et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Critical assessment of methods of protein structure prediction (CASP)—Round XIII
- (2019) Andriy Kryshtafovych et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- High precision in protein contact prediction using fully convolutional neural networks and minimal sequence features
- (2018) David T Jones et al. BIOINFORMATICS
- Combining co-evolution and secondary structure prediction to improve fragment library generation
- (2018) Saulo H P de Oliveira et al. BIOINFORMATICS
- CONFOLD2: improved contact-driven ab initio protein structure modeling
- (2018) Badri Adhikari et al. BMC BIOINFORMATICS
- UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics
- (2018) Cezary Czaplewski et al. NUCLEIC ACIDS RESEARCH
- Clustering huge protein sequence sets in linear time
- (2018) Martin Steinegger et al. Nature Communications
- PconsC4: fast, accurate and hassle-free contact predictions
- (2018) Mirco Michel et al. BIOINFORMATICS
- The Pfam protein families database in 2019
- (2018) Sara El-Gebali et al. NUCLEIC ACIDS RESEARCH
- Protein contact maps: A binary depiction of protein 3D structures
- (2017) Isaac Arnold Emerson et al. PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
- Analysis of deep learning methods for blind protein contact prediction in CASP12
- (2017) Sheng Wang et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model
- (2017) Sheng Wang et al. PLoS Computational Biology
- An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences
- (2017) Su Datt Lam et al. Acta Crystallographica Section D-Structural Biology
- Critical Features of Fragment Libraries for Protein Structure Prediction
- (2017) Raphael Trevizani et al. PLoS One
- UniCon3D:de novoprotein structure prediction using united-residue conformational search via stepwise, probabilistic sampling
- (2016) Debswapna Bhattacharya et al. BIOINFORMATICS
- 3Drefine: an interactive web server for efficient protein structure refinement
- (2016) Debswapna Bhattacharya et al. NUCLEIC ACIDS RESEARCH
- dRHP-PseRA: detecting remote homology proteins using profile-based pseudo protein sequence and rank aggregation
- (2016) Junjie Chen et al. Scientific Reports
- The history of the CATH structural classification of protein domains
- (2015) Ian Sillitoe et al. BIOCHIMIE
- GDFuzz3D: a method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function
- (2015) Michal J. Pietal et al. BIOINFORMATICS
- Customised fragments libraries for protein structure prediction based on structural class annotations
- (2015) Jad Abbass et al. BMC BIOINFORMATICS
- TMFoldRec: a statistical potential-based transmembrane protein fold recognition tool
- (2015) Dániel Kozma et al. BMC BIOINFORMATICS
- Deep learning
- (2015) Yann LeCun et al. NATURE
- The I-TASSER Suite: protein structure and function prediction
- (2015) Jianyi Yang et al. NATURE METHODS
- The Phyre2 web portal for protein modeling, prediction and analysis
- (2015) Lawrence A Kelley et al. Nature Protocols
- Integration of QUARK and I-TASSER for Ab Initio Protein Structure Prediction in CASP11
- (2015) Wenxuan Zhang et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- De novo protein conformational sampling using a probabilistic graphical model
- (2015) Debswapna Bhattacharya et al. Scientific Reports
- Building a Better Fragment Library for De Novo Protein Structure Prediction
- (2015) Saulo H. P. de Oliveira et al. PLoS One
- MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins
- (2014) David T. Jones et al. BIOINFORMATICS
- UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches
- (2014) B. E. Suzek et al. BIOINFORMATICS
- Bhageerath-H: A homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins
- (2014) B Jayaram et al. BMC BIOINFORMATICS
- Lipid14: The Amber Lipid Force Field
- (2014) Callum J. Dickson et al. Journal of Chemical Theory and Computation
- Memoir: template-based structure prediction for membrane proteins
- (2013) Jean-Paul Ebejer et al. NUCLEIC ACIDS RESEARCH
- Relaxation of backbone bond geometry improves protein energy landscape modeling
- (2013) Patrick Conway et al. PROTEIN SCIENCE
- Toward optimal fragment generations forab initioprotein structure assembly
- (2013) Dong Xu et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- High-Resolution Comparative Modeling with RosettaCM
- (2013) Yifan Song et al. STRUCTURE
- Template-based protein structure modeling using the RaptorX web server
- (2012) Morten Källberg et al. Nature Protocols
- ASTRO-FOLD 2.0: An enhanced framework for protein structure prediction
- (2011) A. Subramani et al. AICHE JOURNAL
- Improving the Physical Realism and Structural Accuracy of Protein Models by a Two-Step Atomic-Level Energy Minimization
- (2011) Dong Xu et al. BIOPHYSICAL JOURNAL
- Protein sequence comparison and fold recognition: progress and good-practice benchmarking
- (2011) Johannes Söding et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- A general and efficient Monte Carlo method for sampling intramolecular degrees of freedom of branched and cyclic molecules
- (2011) Jindal K. Shah et al. JOURNAL OF CHEMICAL PHYSICS
- HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
- (2011) Michael Remmert et al. NATURE METHODS
- The Genome Portal of the Department of Energy Joint Genome Institute
- (2011) I. V. Grigoriev et al. NUCLEIC ACIDS RESEARCH
- HMMER web server: interactive sequence similarity searching
- (2011) R. D. Finn et al. NUCLEIC ACIDS RESEARCH
- MEDELLER: homology-based coordinate generation for membrane proteins
- (2010) Sebastian Kelm et al. BIOINFORMATICS
- How significant is a protein structure similarity with TM-score = 0.5?
- (2010) Jinrui Xu et al. BIOINFORMATICS
- pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination
- (2009) Anna Lobley et al. BIOINFORMATICS
- CHARMM: The biomolecular simulation program
- (2009) B. R. Brooks et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Macromolecular Modeling with Rosetta
- (2008) Rhiju Das et al. Annual Review of Biochemistry
- FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps
- (2008) Marco Vassura et al. BIOINFORMATICS
- Reconstruction of 3D Structures From Protein Contact Maps
- (2008) M. Vassura et al. IEEE-ACM Transactions on Computational Biology and Bioinformatics
- SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling
- (2008) Qiang Wang et al. Nature Protocols
- PROMALS3D: a tool for multiple protein sequence and structure alignments
- (2008) Jimin Pei et al. NUCLEIC ACIDS RESEARCH
- Reconstruction of Protein Backbones from the BriX Collection of Canonical Protein Fragments
- (2008) Lies Baeten et al. PLoS Computational Biology
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