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Proteins x Bioinformatics and Computational Biology x clear all

Automated physics-based design of synthetic riboswitches from diverse RNA aptamers

Amin Espah Borujeni, Dennis M. Mishler, Jingzhi Wang, Walker Huso and Howard M. Salis.

in Nucleic Acids Research

January 2016; p ublished online November 2015 .

Journal Article. Subjects: Research Methods in Life Sciences; Bioinformatics and Computational Biology; Proteins; Molecular Biology and Genetics. 8537 words.

Riboswitches are shape-changing regulatory RNAs that bind chemicals and regulate gene expression, directly coupling sensing to cellular actuation. However, it remains unclear how their...

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Computational learning on specificity-determining residue-nucleotide interactions

Ka-Chun Wong, Yue Li, Chengbin Peng, Alan M. Moses and Zhaolei Zhang.

in Nucleic Acids Research

December 2015; p ublished online November 2015 .

Journal Article. Subjects: Proteins; Bioinformatics and Computational Biology; Molecular Biology and Genetics. 6197 words.

The protein–DNA interactions between transcription factors and transcription factor binding sites are essential activities in gene regulation. To decipher the binding codes, it is a...

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ConBind: motif-aware cross-species alignment for the identification of functional transcription factor binding sites

Stefan H. Lelieveld, Judith Schütte, Maurits J.J. Dijkstra, Punto Bawono, Sarah J. Kinston, Berthold Göttgens, Jaap Heringa and Nicola Bonzanni.

in Nucleic Acids Research

May 2016; p ublished online December 2015 .

Journal Article. Subjects: Proteins; Molecular Biology and Genetics; Bioinformatics and Computational Biology. 6488 words.

Eukaryotic gene expression is regulated by transcription factors (TFs) binding to promoter as well as distal enhancers. TFs recognize short, but specific binding sites (TFBSs) that are...

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A deep learning framework for modeling structural features of RNA-binding protein targets

Sai Zhang, Jingtian Zhou, Hailin Hu, Haipeng Gong, Ligong Chen, Chao Cheng and Jianyang Zeng.

in Nucleic Acids Research

February 2016; p ublished online October 2015 .

Journal Article. Subjects: Molecular and Cell Biology; Proteins; Molecular Biology and Genetics; Bioinformatics and Computational Biology. 11261 words.

RNA-binding proteins (RBPs) play important roles in the post-transcriptional control of RNAs. Identifying RBP binding sites and characterizing RBP binding preferences are key steps toward...

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DNA-binding protein prediction using plant specific support vector machines: validation and application of a new genome annotation tool

Graham B. Motion, Andrew J. M. Howden, Edgar Huitema and Susan Jones.

in Nucleic Acids Research

December 2015; p ublished online August 2015 .

Journal Article. Subjects: Proteins; Molecular Biology and Genetics; Bioinformatics and Computational Biology. 8153 words.

There are currently 151 plants with draft genomes available but levels of functional annotation for putative protein products are low. Therefore, accurate computational predictions are...

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Fragment-based modelling of single stranded RNA bound to RNA recognition motif containing proteins

Isaure Chauvot de Beauchene, Sjoerd J. de Vries and Martin Zacharias.

in Nucleic Acids Research

June 2016; p ublished online April 2016 .

Journal Article. Subjects: Proteins; Molecular Biology and Genetics; Research Methods in Life Sciences; Bioinformatics and Computational Biology. 11320 words.

Protein-RNA complexes are important for many biological processes. However, structural modeling of such complexes is hampered by the high flexibility of RNA. Particularly challenging is the...

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Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1

Zhenqing Ye, Zhong Chen, Benjamin Sunkel, Seth Frietze, Tim H.-M. Huang, Qianben Wang and Victor X. Jin.

in Nucleic Acids Research

September 2016; p ublished online July 2016 .

Journal Article. Subjects: Molecular and Cell Biology; Genetics and Genomics; Proteins; Molecular Biology and Genetics; Bioinformatics and Computational Biology. 10443 words.

The compaction of nucleosomal structures creates a barrier for DNA-binding transcription factors (TFs) to access their cognate cis-regulatory elements. Pioneer factors (PFs) such as FOXA1...

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A human transcription factor in search mode

Kevin Hauser, Bernard Essuman, Yiqing He, Evangelos Coutsias, Miguel Garcia-Diaz and Carlos Simmerling.

in Nucleic Acids Research

January 2016; p ublished online December 2015 .

Journal Article. Subjects: Bioinformatics and Computational Biology; Proteins; Molecular Biology and Genetics. 9273 words.

Transcription factors (TF) can change shape to bind and recognize DNA, shifting the energy landscape from a weak binding, rapid search mode to a higher affinity recognition mode. However,...

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The initial step of DNA hairpin folding: a kinetic analysis using fluorescence correlation spectroscopy

Jiho Kim, Sören Doose, Hannes Neuweiler and Markus Sauer.

in Nucleic Acids Research

January 2006; p ublished online January 2006 .

Journal Article. Subjects: Proteins; Molecular Biology and Genetics; Bioinformatics and Computational Biology. 9597 words.

Conformational fluctuations of single-stranded DNA (ssDNA) oligonucleotides were studied in aqueous solution by monitoring contact-induced fluorescence quenching of the oxazine fluorophore...

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Leveraging cross-link modification events in CLIP-seq for motif discovery

Emad Bahrami-Samani, Luiz O.F. Penalva, Andrew D. Smith and Philip J. Uren.

in Nucleic Acids Research

January 2015; p ublished online December 2014 .

Journal Article. Subjects: Proteins; Molecular Biology and Genetics; Bioinformatics and Computational Biology; Research Methods in Life Sciences. 6246 words.

High-throughput protein–RNA interaction data generated by CLIP-seq has provided an unprecedented depth of access to the activities of RNA-binding proteins (RBPs), the key players in co- and...

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MMB-GUI: a fast morphing method demonstrates a possible ribosomal tRNA translocation trajectory

Alex Tek, Andrei A. Korostelev and Samuel Coulbourn Flores.

in Nucleic Acids Research

January 2016; p ublished online December 2015 .

Journal Article. Subjects: Bioinformatics and Computational Biology; Proteins; Molecular Biology and Genetics. 7487 words.

Easy-to-use macromolecular viewers, such as UCSF Chimera, are a standard tool in structural biology. They allow rendering and performing geometric operations on large complexes, such as...

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A novel method for improved accuracy of transcription factor binding site prediction

Abdullah M Khamis, Olaa Motwalli, Romina Oliva, Boris R Jankovic, Yulia A Medvedeva, Haitham Ashoor, Magbubah Essack, Xin Gao and Vladimir B Bajic.

in Nucleic Acids Research

July 2018; p ublished online April 2018 .

Journal Article. Subjects: Proteins; Molecular Biology and Genetics; Bioinformatics and Computational Biology. 9277 words.

Abstract

Identifying transcription factor (TF) binding sites (TFBSs) is important in the computational inference of gene regulation. Widely used computational...

Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes

Mario Pujato, Fabien Kieken, Amanda A. Skiles, Nikos Tapinos and Andras Fiser.

in Nucleic Acids Research

December 2014; p ublished online November 2014 .

Journal Article. Subjects: Proteins; Molecular Biology and Genetics; Bioinformatics and Computational Biology. 10068 words.

Proper cell functioning depends on the precise spatio-temporal expression of its genetic material. Gene expression is controlled to a great extent by sequence-specific transcription factors...

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Prediction of nucleic acid binding probability in proteins: a neighboring residue network based score

Zhichao Miao and Eric Westhof.

in Nucleic Acids Research

June 2015; p ublished online May 2015 .

Journal Article. Subjects: Proteins; Molecular Biology and Genetics; Bioinformatics and Computational Biology. 7782 words.

We describe a general binding score for predicting the nucleic acid binding probability in proteins. The score is directly derived from physicochemical and evolutionary features and...

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Probing binding hot spots at protein–RNA recognition sites

Amita Barik, Chandran Nithin, Naga Bhushana Rao Karampudi, Sunandan Mukherjee and Ranjit Prasad Bahadur.

in Nucleic Acids Research

January 2016; p ublished online September 2015 .

Journal Article. Subjects: Bioinformatics and Computational Biology; Proteins; Molecular Biology and Genetics. 6393 words.

We use evolutionary conservation derived from structure alignment of polypeptide sequences along with structural and physicochemical attributes of protein–RNA interfaces to probe the...

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Protein binding site prediction using an empirical scoring function

Shide Liang, Chi Zhang, Song Liu and Yaoqi Zhou.

in Nucleic Acids Research

August 2006; p ublished online August 2006 .

Journal Article. Subjects: Proteins; Molecular Biology and Genetics; Bioinformatics and Computational Biology. 8695 words.

Most biological processes are mediated by interactions between proteins and their interacting partners including proteins, nucleic acids and small molecules. This work establishes a method...

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Protein complex compositions predicted by structural similarity

Fred P. Davis, Hannes Braberg, Min-Yi Shen, Ursula Pieper, Andrej Sali and M.S. Madhusudhan.

in Nucleic Acids Research

January 2006; p ublished online January 2006 .

Journal Article. Subjects: Proteins; Molecular Biology and Genetics; Bioinformatics and Computational Biology. 7054 words.

Proteins function through interactions with other molecules. Thus, the network of physical interactions among proteins is of great interest to both experimental and computational...

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PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration

Jeroen Crappé, Elvis Ndah, Alexander Koch, Sandra Steyaert, Daria Gawron, Sarah De Keulenaer, Ellen De Meester, Tim De Meyer, Wim Van Criekinge, Petra Van Damme and Gerben Menschaert.

in Nucleic Acids Research

March 2015; p ublished online December 2014 .

Journal Article. Subjects: Genetics and Genomics; Research Methods in Life Sciences; Bioinformatics and Computational Biology; Proteins; Molecular Biology and Genetics. 6340 words.

An increasing amount of studies integrate mRNA sequencing data into MS-based proteomics to complement the translation product search space. However, several factors, including extensive...

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RiboAbacus: a model trained on polyribosome images predicts ribosome density and translational efficiency from mammalian transcriptomes

Fabio Lauria, Toma Tebaldi, Lorenzo Lunelli, Paolo Struffi, Pamela Gatto, Andrea Pugliese, Maurizio Brigotti, Lorenzo Montanaro, Yari Ciribilli, Alberto Inga, Alessandro Quattrone, Guido Sanguinetti and Gabriella Viero.

in Nucleic Acids Research

December 2015; p ublished online August 2015 .

Journal Article. Subjects: Bioinformatics and Computational Biology; Proteins; Molecular Biology and Genetics. 11372 words.

Fluctuations in mRNA levels only partially contribute to determine variations in mRNA availability for translation, producing the well-known poor correlation between transcriptome and...

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ROTS: reproducible RNA-seq biomarker detector—prognostic markers for clear cell renal cell cancer

Fatemeh Seyednasrollah, Krista Rantanen, Panu Jaakkola and Laura L. Elo.

in Nucleic Acids Research

January 2016; p ublished online August 2015 .

Journal Article. Subjects: Proteins; Molecular Biology and Genetics; Bioinformatics and Computational Biology. 5032 words.

Recent comprehensive assessments of RNA-seq technology support its utility in quantifying gene expression in various samples. The next step of rigorously quantifying differences between...

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