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The MULTICOM toolbox for protein structure prediction

Jianlin Cheng, Jilong Li, Zheng Wang, Jesse Eickholt, Xin Deng
2012 BMC Bioinformatics  
Results: To meet the need, we have developed a comprehensive MULTICOM toolbox consisting of a set of protein structure and structural feature prediction tools.  ...  In order to facilitate bioinformatics research and technological development in the field, we have made the MULTICOM toolbox freely available as web services and/or software packages for academic use and  ...  Acknowledgements The work is partially supported by a NIH grant (5R01GM093123) to JC, a NLM fellowship to JE, and a Shumaker fellowship to ZW.  ... 
doi:10.1186/1471-2105-13-65 pmid:22545707 pmcid:PMC3495398 fatcat:ngv7ac7pzjcjfjqf4cq5nw2daq

MULTICOM2 open-source protein structure prediction system powered by deep learning and distance prediction

Tianqi Wu, Jian Liu, Zhiye Guo, Jie Hou, Jianlin Cheng
2021 Scientific Reports  
The source code of MULTICOM2 is freely available at https://github.com/multicom-toolbox/multicom/tree/multicom_v2.0.  ...  However, there are still few open-source comprehensive protein structure prediction packages publicly available in the field.  ...  Acknowledgements We wish to thank CASP organizers and predictors for sharing the data used in this work.  ... 
doi:10.1038/s41598-021-92395-6 pmid:34162922 pmcid:PMC8222248 fatcat:36sfln4wujhodguwmyab4o4fve

Improving protein tertiary structure prediction by deep learning and distance prediction in CASP14

Jian Liu, Tianqi Wu, Zhiye Guo, Jie Hou, Jianlin Cheng
2021 Proteins: Structure, Function, and Bioinformatics  
Inspired by the advances, we improve our CASP14 MULTICOM protein structure prediction system by incorporating three new components: (1) a new deep learning-based protein inter-residue distance predictor  ...  The structural model quality assessment works well on targets for which enough good models can be predicted, but it may perform poorly when only a few good models are predicted for a hard target and the  ...  The results confirm that the distance-based protein structure prediction can universally address the protein structure prediction problem.  ... 
doi:10.1002/prot.26186 pmid:34291486 pmcid:PMC8671168 fatcat:pygxoy2eznfd3hgyhbp73z6xkq

Analysis of several key factors influencing deep learning-based inter-residue contact prediction

2019 Bioinformatics  
Deep learning has become the dominant technology for protein contact prediction.  ...  /multicom-toolbox/DNCON2/.  ...  Acknowledgements We thank CASP13 organizers for making the data available for evaluation and the reviewers for valuable suggestions.  ... 
doi:10.1093/bioinformatics/btz679 pmid:31504181 pmcid:PMC7703788 fatcat:hngd5dxlt5exbcwadskicjgr3a

Deep Learning-Based Advances in Protein Structure Prediction

Subash C Pakhrin, Bikash Shrestha, Badri Adhikari, Dukka B KC
2021 International Journal of Molecular Sciences  
Finally, we provide an outlook and possible future research directions for DL-based approaches in the protein structure prediction arena.  ...  We also highlight some end-to-end DL-based approaches for protein structure prediction approaches.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ijms22115553 pmid:34074028 fatcat:jzlwbnvdkzf5ta3h55ki7ul5ia

SAXSDom: Modeling multi-domain protein structures using small-angle X-ray scattering data [article]

Jie Hou, Badri Adhikari, John J. Tanner, Jianlin Cheng
2019 bioRxiv   pre-print
The source code and tool packages are available at http://github.com/multicom-toolbox/SAXSDom.  ...  Some multidomain proteins can be challenging for protein structure modeling, particularly those for which templates can be found for the domains but not for the entire sequence.  ...  In our work, the domain structures for these 73 proteins were predicted by MULTICOM tertiary structure prediction method and then further assembled using our model protocol.  ... 
doi:10.1101/559617 fatcat:bj3oreckwzaaja52h2xwzetip4

Deep convolutional neural networks for predicting the quality of single protein structural models [article]

Jie Hou, Renzhi Cao, Jianlin Cheng
2019 bioRxiv   pre-print
AbstractPredicting the global quality and local (residual-specific) quality of a single protein structural model is important for protein structure prediction and application.  ...  The source code and executable of our methods are available at: https://github.com/multicom-toolbox/DeepCovQA  ...  Acknowledgements The work was partially supported by an NIH grant (R01GM093123) and two NSF grants (DBI1759934 & IIS1763246) to JC.  ... 
doi:10.1101/590620 fatcat:6sjhw4is2fdrjgsq4i35mmfcom

CONFOLD2: Improved contact-driven ab initio protein structure modeling [article]

Badri Adhikari, Jianlin Cheng
2017 bioRxiv   pre-print
CONFOLD2 is publicly available at https://github.com/multicom-toolbox/CONFOLD2/.  ...  Results: We develop an improved contact-driven protein modeling method, CONFOLD2, and study how it may be effectively used for ab initio protein structure prediction with predicted contacts as input.  ...  Structure predictions using 115 some recently available contact prediction datasets, show that the for most protein 116 sequences CONFOLD2 is able to capture the structural fold of the protein. 39 equal  ... 
doi:10.1101/228460 fatcat:zixbvxoghzhhnoqtcgvczlrtya

DNCON2_Inter: predicting interchain contacts for homodimeric and homomultimeric protein complexes using multiple sequence alignments of monomers and deep learning

Farhan Quadir, Raj S. Roy, Randal Halfmann, Jianlin Cheng
2021 Scientific Reports  
Allowing true-positive predictions within two residue shifts, the best average precision was obtained for the Top-L/10 predictions of 22.9% for homodimers and 17.0% for higher-order homomultimers.  ...  We also developed Con_Complex, a complex structure reconstruction tool that uses predicted contacts to produce the structure of the complex.  ...  Diagram describing how the input PDB file was pre-processed using the MULTICOM TOOLBOX to clean up the PDB files. If no DSSP is available, the PDB was removed from our list.  ... 
doi:10.1038/s41598-021-91827-7 pmid:34112907 fatcat:ny43ocaxkvfu3dvgrl63rzxs3u

Predicting interchain contacts for homodimeric and homomultimeric protein complexes using multiple sequence alignments of monomers and deep learning [article]

Farhan Quadir, Raj Shekhor Roy, Randal Halfmann, Jianlin Cheng
2020 bioRxiv   pre-print
We show that the predicted contacts can be used to accurately construct the structure of some complexes.  ...  Allowing true-positive predictions within two residue shifts, the best average precision was obtained for the Top-L/10 predictions of DNCON2: 22.9% for homodimers, and 17.0% for higher order homomultimers  ...  file was pre-processed using the MULTICOM TOOLBOX to clean up the PDB files.  ... 
doi:10.1101/2020.11.09.373878 fatcat:4owvnroecbf4dfmsaqex7uxzlu

CONFOLD2: improved contact-driven ab initio protein structure modeling

Badri Adhikari, Jianlin Cheng
2018 BMC Bioinformatics  
The source code of CONFOLD2 is publicly available at https:// github.com/multicom-toolbox/CONFOLD2/.  ...  CONFOLD2 obtains an average reconstruction accuracy of 0.57 TM-score for the 150 proteins in the PSICOV contact prediction dataset.  ...  We would like to thank the RCSS team for their infrastructure and technical support.  ... 
doi:10.1186/s12859-018-2032-6 pmid:29370750 pmcid:PMC5784681 fatcat:ajk4hk2ntjbfpj355u5k2fbfd4

SMDB: SOYBEAN MARKER DATABASE

Ashwani Kumar, Abhay Pratap, Urvashi Udar, Rajinder Singh Chauhan, Tiratha Raj Singh
2014 International Journal for Computational Biology  
Hence understanding the plant genome specific databases for acquiring specific information is the demand of time for crop improvement and research programmes.  ...  Along with this it also furnishes gene level information for various functional categories such as transcription factor, disease resistant varieties, heat shock protein, genetically modified strain of  ...  The Protein Data Bank (PDB) was used to predict tertiary structure of each transcription factor and predicted structure is visualised through JMOL.  ... 
doi:10.34040/ijcb.3.2.2014.27 fatcat:icqlqx7zmzadfbuzo4sgbqxsgi

ConEVA: a toolbox for comprehensive assessment of protein contacts

Badri Adhikari, Jackson Nowotny, Debswapna Bhattacharya, Jie Hou, Jianlin Cheng
2016 BMC Bioinformatics  
It is also observed that for almost all globular proteins, the quality of contact prediction dictates the accuracy of structure prediction.  ...  In recent years, successful contact prediction methods and contact-guided ab initio protein structure prediction methods have highlighted the importance of incorporating contact information into protein  ...  Funding This work has been supported in part by the US National Institutes of Health 10 (NIH) grant (R01GM093123) to J.C.  ... 
doi:10.1186/s12859-016-1404-z pmid:27923350 pmcid:PMC5142288 fatcat:nru32vpkofglhozqfdqvzg7biq

DNCON2: Improved protein contact prediction using two-level deep convolutional neural networks [article]

Badri Adhikari, Jie Hou, Jianlin Cheng
2017 bioRxiv   pre-print
Its source code is available at https://github.com/multicom-toolbox/DNCON2/.  ...  These contacts, predicted using a variety of coevolution-based and machine learning methods, are the key contributors to the recent progress in ab initio protein structure prediction, as demonstrated in  ...  We would like to thank the RCSS team for their infrastructure and technical support.  ... 
doi:10.1101/222893 fatcat:iexvncmpenfh5cfiqu6cp2456a

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Julia Koehler Leman, Brian D. Weitzner, Steven M. Lewis, Jared Adolf-Bryfogle, Nawsad Alam, Rebecca F. Alford, Melanie Aprahamian, David Baker, Kyle A. Barlow, Patrick Barth, Benjamin Basanta, Brian J. Bender (+96 others)
2020 Nature Methods  
The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide.  ...  Here we review tools developed in the last 5 years, including over 80 methods. We discuss improvements to the score function, user interfaces and usability.  ...  RosettaMP toolkit 147 : mp_score, mp_transform, mp_mutate_relax, helix_from_sequence Jeffrey Gray, Richard Bonneau mp_lipid_acc 148 Richard Bonneau mp_domain_assembly 149 Richard Bonneau RosettaCM for  ... 
doi:10.1038/s41592-020-0848-2 pmid:32483333 pmcid:PMC7603796 fatcat:wmspe6dzm5andneitqur5lpniy
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