Detalhe da pesquisa
1.
Multiple sequence alignment-based RNA language model and its application to structural inference.
Nucleic Acids Res
; 52(1): e3, 2024 Jan 11.
Artigo
em Inglês
| MEDLINE | ID: mdl-37941140
2.
Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives.
Brief Bioinform
; 23(3)2022 05 13.
Artigo
em Inglês
| MEDLINE | ID: mdl-35348613
3.
Predicting RNA distance-based contact maps by integrated deep learning on physics-inferred secondary structure and evolutionary-derived mutational coupling.
Bioinformatics
; 38(16): 3900-3910, 2022 08 10.
Artigo
em Inglês
| MEDLINE | ID: mdl-35751593
4.
SPOT-Contact-LM: improving single-sequence-based prediction of protein contact map using a transformer language model.
Bioinformatics
; 38(7): 1888-1894, 2022 03 28.
Artigo
em Inglês
| MEDLINE | ID: mdl-35104320
5.
RNAcmap: a fully automatic pipeline for predicting contact maps of RNAs by evolutionary coupling analysis.
Bioinformatics
; 37(20): 3494-3500, 2021 Oct 25.
Artigo
em Inglês
| MEDLINE | ID: mdl-34021744
6.
SPOT-1D-Single: improving the single-sequence-based prediction of protein secondary structure, backbone angles, solvent accessibility and half-sphere exposures using a large training set and ensembled deep learning.
Bioinformatics
; 37(20): 3464-3472, 2021 Oct 25.
Artigo
em Inglês
| MEDLINE | ID: mdl-33983382
7.
Improved RNA secondary structure and tertiary base-pairing prediction using evolutionary profile, mutational coupling and two-dimensional transfer learning.
Bioinformatics
; 37(17): 2589-2600, 2021 Sep 09.
Artigo
em Inglês
| MEDLINE | ID: mdl-33704363
8.
High-throughput mapping of RNA solvent accessibility at the single-nucleotide resolution by RtcB ligation between a fixed 5'-OH-end linker and unique 3'-P-end fragments from hydroxyl radical cleavage.
RNA Biol
; 19(1): 1179-1189, 2022 01.
Artigo
em Inglês
| MEDLINE | ID: mdl-36369947
9.
Identifying molecular recognition features in intrinsically disordered regions of proteins by transfer learning.
Bioinformatics
; 36(4): 1107-1113, 2020 02 15.
Artigo
em Inglês
| MEDLINE | ID: mdl-31504193
10.
SPOT-Fold: Fragment-Free Protein Structure Prediction Guided by Predicted Backbone Structure and Contact Map.
J Comput Chem
; 41(8): 745-750, 2020 03 30.
Artigo
em Inglês
| MEDLINE | ID: mdl-31845383
11.
Improving prediction of protein secondary structure, backbone angles, solvent accessibility and contact numbers by using predicted contact maps and an ensemble of recurrent and residual convolutional neural networks.
Bioinformatics
; 35(14): 2403-2410, 2019 07 15.
Artigo
em Inglês
| MEDLINE | ID: mdl-30535134
12.
Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networks.
Bioinformatics
; 34(23): 4039-4045, 2018 12 01.
Artigo
em Inglês
| MEDLINE | ID: mdl-29931279
13.
SPOT-Peptide: Template-Based Prediction of Peptide-Binding Proteins and Peptide-Binding Sites.
J Chem Inf Model
; 59(2): 924-930, 2019 02 25.
Artigo
em Inglês
| MEDLINE | ID: mdl-30698427
14.
SPOT-ligand 2: improving structure-based virtual screening by binding-homology search on an expanded structural template library.
Bioinformatics
; 33(8): 1238-1240, 2017 04 15.
Artigo
em Inglês
| MEDLINE | ID: mdl-28057679
15.
Non-steroidal anti-inflammatories and the development of analgesic nephropathy: a systematic review.
Ren Fail
; 38(9): 1328-1334, 2016 Oct.
Artigo
em Inglês
| MEDLINE | ID: mdl-27494231
16.
MARS and RNAcmap3: The Master Database of All Possible RNA Sequences Integrated with RNAcmap for RNA Homology Search.
Genomics Proteomics Bioinformatics
; 22(1)2024 May 09.
Artigo
em Inglês
| MEDLINE | ID: mdl-38872612
17.
Reaching alignment-profile-based accuracy in predicting protein secondary and tertiary structural properties without alignment.
Sci Rep
; 12(1): 7607, 2022 05 09.
Artigo
em Inglês
| MEDLINE | ID: mdl-35534620
18.
High-throughput split-protein profiling by combining transposon mutagenesis and regulated protein-protein interactions with deep sequencing.
Int J Biol Macromol
; 203: 543-552, 2022 Apr 01.
Artigo
em Inglês
| MEDLINE | ID: mdl-35120933
19.
Getting to Know Your Neighbor: Protein Structure Prediction Comes of Age with Contextual Machine Learning.
J Comput Biol
; 27(5): 796-814, 2020 05.
Artigo
em Inglês
| MEDLINE | ID: mdl-31390220
20.
Systematic Analysis of REBASE Identifies Numerous Type I Restriction-Modification Systems with Duplicated, Distinct hsdS Specificity Genes That Can Switch System Specificity by Recombination.
mSystems
; 5(4)2020 Jul 28.
Artigo
em Inglês
| MEDLINE | ID: mdl-32723795