Integrated structure-based protein interface prediction
BMC Bioinformatics, 2022 Background Identifying protein interfaces can inform how proteins interact with their binding partners, uncover the regulatory mechanisms that control biological functions and guide the development of novel therapeutic agents.
M. Walder +6 more
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DeepDist: real-value inter-residue distance prediction with deep residual convolutional network
BMC Bioinformatics, 2021 Background Driven by deep learning, inter-residue contact/distance prediction has been significantly improved and substantially enhanced ab initio protein structure prediction.
Tianqi Wu +3 more
doaj +1 more source
Non-H3 CDR template selection in antibody modeling through machine learning [PDF]
PeerJ, 2019 Antibodies are proteins generated by the adaptive immune system to recognize and counteract a plethora of pathogens through specific binding. This adaptive binding is mediated by structural diversity in the six complementary determining region (CDR ...
Xiyao Long +2 more
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Water in protein structure prediction [PDF]
Proceedings of the National Academy of Sciences, 2004 Proteins have evolved to use water to help guide folding. A physically motivated, nonpairwise-additive model of water-mediated interactions added to a protein structure prediction Hamiltonian yields marked improvement in the quality of structure prediction for larger proteins.
Papoian, G A +4 more
openaire +3 more sources
FALCON2: a web server for high-quality prediction of protein tertiary structures
BMC Bioinformatics, 2021 Background Accurate prediction of protein tertiary structures is highly desired as the knowledge of protein structures provides invaluable insights into protein functions.
Lupeng Kong +4 more
doaj +1 more source
CirPred, the first structure modeling and linker design system for circularly permuted proteins
BMC Bioinformatics, 2021 Background This work aims to help develop new protein engineering techniques based on a structural rearrangement phenomenon called circular permutation (CP), equivalent to connecting the native termini of a protein followed by creating new termini at ...
Teng-Ruei Chen +4 more
doaj +1 more source
Prediction of protein structure [PDF]
Current Biology, 2000 Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.Nucleic Acids Res 1997, 25:3389-3402Bowie JU, Eisenberg D: Inverted protein structure prediction.
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Structure-aware protein-protein interaction site prediction using deep graph convolutional network
, 2021 MOTIVATION: Protein-protein interactions (PPI) play crucial roles in many biological processes, and identifying PPI sites is an important step for mechanistic understanding of diseases and design of novel drugs. Since experimental approaches for PPI site
Zhou, Yaoqi +4 more
core +1 more source
CASP11--An Evaluation of a Modular BCL::Fold-Based Protein Structure Prediction Pipeline. [PDF]
PLoS ONE, 2016 In silico prediction of a protein's tertiary structure remains an unsolved problem. The community-wide Critical Assessment of Protein Structure Prediction (CASP) experiment provides a double-blind study to evaluate improvements in protein structure ...
Axel W Fischer +7 more
doaj +1 more source
Prediction of Structure, Function, and Spectroscopic Properties of G-Protein-Coupled Receptors: Methods and Applications [PDF]
, 2004 G-protein-coupled receptors are of great pharmaceutical interest, comprising the majority of targets for currently marketed drugs. The theme of my thesis is the development of the structure prediction method, MembStruk, for the superfamily of G-protein ...
Trabanino, Rene Jouvanni
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