Demo Data from VLDB 2026 / reviewers in the wild / expert
Raj S. Roy
dblp:310/0215
· DBLP profile ↗
1ranked-venue papers
1as first author
1since 2021 · last 2022
0000-0002-2400-7210ORCID · reported
Domains — the database's venue-derived domains; a paper can count in several
Applied, interdisciplinary, general and emerging computing · 1 · 1 first-author · 1 since 2021
Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.
| Interdisciplinary, comprehensive, and emerging computing
1 paper |
Bioinformatics and computational biology · 100% |
Topics — the 2 heaviest of 2, each with the papers that count most for it
| Topic | Weight | Papers | Last | Evidence papers |
|---|---|---|---|---|
Bioinformatics and computational biology
protein structure prediction |
0.6 | 1 | 2022 | A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers · Bioinform. 2022 |
Bioinformatics and computational biology › protein structure analysis
quaternary structure |
0.6 | 1 | 2022 | A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers · Bioinform. 2022 |
Methods — techniques the papers use, named apart from their topics
multiple sequence alignment · 0.6deep dilated convolutional residual network · 0.6co-evolutionary signal · 0.6
| Year | Publication | Venue | Position |
|---|---|---|---|
| 2022 | A deep dilated convolutional residual network for predicting interchain contacts of protein homodimersabstractMOTIVATION: Deep learning has revolutionized protein tertiary structure prediction recently. The cutting-edge deep learning methods such as AlphaFold can predict high-accuracy tertiary structures for most individual protein chains. However, the accuracy of predicting quaternary structures of protein complexes consisting of multiple chains is still relatively low due to lack of advanced deep learning methods in the field. Because interchain residue-residue contacts can be used as distance restraints to guide quaternary structure modeling, here we develop a deep dilated convolutional residual network method (DRCon) to predict interchain residue-residue contacts in homodimers from residue-residue co-evolutionary signals derived from multiple sequence alignments of monomers, intrachain residue-residue contacts of monomers extracted from true/predicted tertiary structures or predicted by deep learning, and other sequence and structural features. RESULTS: Tested on three homodimer test datasets (Homo_std dataset, DeepHomo dataset and CASP-CAPRI dataset), the precision of DRCon for top L/5 interchain contact predictions (L: length of monomer in a homodimer) is 43.46%, 47.10% and 33.50% respectively at 6 Å contact threshold, which is substantially better than DeepHomo and DNCON2_inter and similar to Glinter. Moreover, our experiments demonstrate that using predicted tertiary structure or intrachain contacts of monomers in the unbound state as input, DRCon still performs well, even though its accuracy is lower than using true tertiary structures in the bound state are used as input. Finally, our case study shows that good interchain contact predictions can be used to build high-accuracy quaternary structure models of homodimers. AVAILABILITY AND IMPLEMENTATION: The source code of DRCon is available at https://github.com/jianlin-cheng/DRCon. The datasets are available at https://zenodo.org/record/5998532#.YgF70vXMKsB. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Raj S. Roy, Farhan Quadir, Elham Soltanikazemi, Jianlin Cheng |
Bioinform. | 1 |