Log in first for optimal use of all functions!

    Surface-based protein domains retrieval methods from a SHREC2021 challenge (English)

    In: Journal of Molecular Graphics and Modelling ; 111 ; 2021
    • ISSN:
      1093-3263
    • Article (Journal)  /  Electronic Resource

    How to get this title?

    Check access
    Download

    Download is DRM protected.

    Commercial Copyright fee: €36.00 Basic fee: €4.00 Total price: €40.00
    Academic Copyright fee: €36.00 Basic fee: €2.00 Total price: €38.00

    Export, share and cite

    Abstract Proteins are essential to nearly all cellular mechanism and the effectors of the cells activities. As such, they often interact through their surface with other proteins or other cellular ligands such as ions or organic molecules. The evolution generates plenty of different proteins, with unique abilities, but also proteins with related functions hence similar 3D surface properties (shape, physico-chemical properties, …). The protein surfaces are therefore of primary importance for their activity. In the present work, we assess the ability of different methods to detect such similarities based on the geometry of the protein surfaces (described as 3D meshes), using either their shape only, or their shape and the electrostatic potential (a biologically relevant property of proteins surface). Five different groups participated in this contest using the shape-only dataset, and one group extended its pre-existing method to handle the electrostatic potential. Our comparative study reveals both the ability of the methods to detect related proteins and their difficulties to distinguish between highly related proteins. Our study allows also to analyze the putative influence of electrostatic information in addition to the one of protein shapes alone. Finally, the discussion permits to expose the results with respect to ones obtained in the previous contests for the extended method. The source codes of each presented method have been made available online.

    Graphical abstract Display Omitted

    Table of contents – Volume 111

    Show all volumes and issues

    The tables of contents are generated automatically and are based on the data records of the individual contributions available in the index of the TIB portal. The display of the Tables of Contents may therefore be incomplete.

    Binding interaction of a potential statin with β-lactoglobulin: An in silico approach
    Baruah, Indrani / Borgohain, Gargi et al. | 2021
    Structural anomalies in a published NMR-derived structure of IRAK-M
    Poelman, Hessel / Ippel, Hans / Gürkan, Berke / Boelens, Rolf / Vriend, Gert / Veer, Cornelis van ‘t / Lutgens, Esther / Nicolaes, Gerry A.F. et al. | 2021
    First principles study on electronic properties and oxygen evolution mechanism of 2D bimetallic N-doped graphene
    Hou, Guoyu / Song, Yubao / Ma, Xinxia / Chu, Fenghong / Wu, Maoliang / Wang, Daolei / Wu, Jiang / Qi, Yongfeng / Wu, Cuicui / Xiong, Muchun et al. | 2021
    Nano-porous C4N as a toxic pesticide's scavenger: A quantum chemical approach
    Asif, Misbah / Sajid, Hasnain / Ayub, Khurshid / Khan, Adnan Ali / Ahmad, Rashid / Ans, Muhammad / Mahmood, Tariq et al. | 2021
    In silico development of new PET radiopharmaceuticals from mTOR inhibitors
    Ferino-Pérez, Anthuan / Vélayoudom, Fritz-Line / Belia, Lyonel / Glaude, Eddy-Laurent / Gaspard, Sarra / Jáuregui-Haza, Ulises J. et al. | 2021
    Molecular dynamics simulations reveal the plausible agonism/antagonism mechanism by steroids on androgen receptor mutations
    Kocak, Abdulkadir / Yildiz, Muslum et al. | 2021
    Ligand-based G Protein Coupled Receptor pharmacophore modeling: Assessing the role of ligand function in model development
    Castleman, P. / Szwabowski, G. / Bowman, D. / Cole, J. / Parrill, A.L. / Baker, D.L. et al. | 2021
    Homology modelling of Trypanosoma brucei major surface proteases and molecular docking of variant surface glycoproteins and inhibitor ligands for drug design
    Marufu, Lucky / Coetzer, Theresa.H.T. et al. | 2021
    Conformational exploration of RbgA using molecular dynamics: Possible implications in ribosome maturation and GTPase activity in different nucleotide bound states
    Upendra, N. / Krishnaveni, S. et al. | 2021
    R•-hole interactions of group IV-VII radical-containing molecules: A comparative study
    Ibrahim, Mahmoud A.A. / Mohamed, Yasmeen A.M. / Abd Elhafez, Heba S.M. / Shehata, Mohammed N.I. / Soliman, Mahmoud E.S. / Ahmed, Muhammad Naeem / Abd El-Mageed, H.R. / Moussa, Nayra A.M. et al. | 2021
    Parallel-slipped π−π electron-donor−acceptor in adsorption process: Molecular dynamics simulation
    Chen, Zhen / Ma, Wei / Lu, Guang / Hu, Jinglu / Zhang, Zhe / Wang, Baodong / Cheng, Zihong / Pan, Yuzhen et al. | 2021
    Exploiting the glycan receptor-binding site of PltB subunit in salmonella typhi toxin for novel inhibitors: An in-silico approach
    Marondedze, Ephraim Felix / Govender, Penny Poomani et al. | 2021
    N-doped direction-dependent electronic and mechanical properties of single-walled carbon nanotube (SWCNT) from a first-principles density functional theory (DFT) and MD-simulation
    Singh, Y.T. / Patra, P.K. / Obodo, K.O. / Saad H.-E, M. Musa / Rai, D.P. et al. | 2021
    Machine learning and deep learning enabled fuel sooting tendency prediction from molecular structure
    Li, Runzhao / Herreros, Jose Martin / Tsolakis, Athanasios / Yang, Wenzhao et al. | 2021
    On the mechanical properties and fracture analysis of polymer nanocomposites reinforced by functionalized silicon carbide nanotubes: A molecular dynamics investigation
    Eghbalian, M. / Ansari, R. / Haghighi, S. et al. | 2021
    The role of temperature in the binding of the disordered epitope region of human thrombopoietin to antibody: A molecular dynamics simulations study
    Badaya, Apoorva / Sasidhar, Yellamraju U. et al. | 2021
    Enhancement of absorption capacity, optical and non-linear optical properties of graphene oxide nanosheet
    Foadin, Crevain Souop Tala / Tchangnwa Nya, Fridolin / Malloum, Alhadji / Conradie, Jeanet et al. | 2021
    Surface-based protein domains retrieval methods from a SHREC2021 challenge
    Langenfeld, Florent / Aderinwale, Tunde / Christoffer, Charles / Shin, Woong-Hee / Terashi, Genki / Wang, Xiao / Kihara, Daisuke / Benhabiles, Halim / Hammoudi, Karim / Cabani, Adnane et al. | 2021
    Mechanistic insights into the dehydrogenation of formaldehyde, formic acid and methanol using the Pt4 cluster as a promising catalyst
    Phan, Thuy Thi / Dao, Linh Thao Thi / Giang, Ly Phương Thi / Nguyen, Mo Thi / Nguyen, Hue Minh Thi et al. | 2021
    QSAR and deep learning model for virtual screening of potential inhibitors against Inosine 5’ Monophosphate dehydrogenase (IMPDH) of Cryptosporidium parvum
    Asmare, Misgana Mengistu / Nitin, Nitin / Yun, Soon-IL / Mahapatra, Rajani Kanta et al. | 2021
    In-silico design of peptides for inhibition of HLA-A*03-KLIETYFSK complex as a new drug design for treatment of multiples sclerosis disease
    Ghobadi, Zahra / Mahnam, Karim / Shakhsi-Niaei, Mostafa et al. | 2021
    II-VI core/shell quantum dots and doping with transition metal ions as a means of tuning the magnetoelectronic properties of CdS/ZnS core/shell QDs: A DFT study
    Malik, Pragati / Thareja, Rakhi / Singh, Jyoti / Kakkar, Rita et al. | 2021
    Structures, binding energies and non-covalent interactions of furan clusters
    Malloum, Alhadji / Conradie, Jeanet et al. | 2021
    Sc-functionalized porphyrin-like porous fullerene for CO2 storage and separation: A first-principles evaluation
    Esrafili, Mehdi D. / Mousavian, Parisasadat et al. | 2021
    The effect of external salts on the aggregation of the multiheaded surfactants: All-atom molecular dynamics studies
    Dash, Sandeep / Chowdhury, Unmesh D. / Bhargava, B.L. et al. | 2021
    Identification of potent food constituents as SARS-CoV-2 papain-like protease modulators through advanced pharmacoinformatics approaches
    Bhowmick, Shovonlal / Saha, Achintya / AlFaris, Nora Abdullah / ALTamimi, Jozaa Zaidan / ALOthman, Zeid A. / Aldayel, Tahany Saleh / Wabaidur, Saikh Mohammad / Islam, Md Ataul et al. | 2021
    High velocity impact analysis of free-free carbon nanotubes
    Ajori, S. / Ameri, A. / Ansari, R. et al. | 2021
    Editorial Board
    | 2022
    Molecular dynamics simulation of edge crack propagation in single crystalline alpha quartz
    Molaei, Fatemeh et al. | 2021
    The steroid mometasone alters protein containing lung surfactant monolayers in a concentration-dependent manner
    Islam, Mohammad Zohurul / Hossain, Sheikh I. / Deplazes, Evelyne / Saha, Suvash C. et al. | 2021
    Computational study of the interaction of heavy metal ions, Cd(II), Hg(II), and Pb(II) on lignin matrices
    Santos, Thifany Justo / Paggiaro, Juliana / Cabral Silva Pimentel, Helhe Daiany / Karla dos Santos Pereira, Anna / Cavallini, Grasiele Soares / Pereira, Douglas Henrique et al. | 2021
    Exploring sodium glucose cotransporter (SGLT2) inhibitors with machine learning approach: A novel hope in anti-diabetes drug discovery
    Moinul, Md / Amin, Sk Abdul / Kumar, Prabhat / Patil, Umesh Kumar / Gajbhiye, Asmita / Jha, Tarun / Gayen, Shovanlal et al. | 2021
    New insights into NO adsorption on alkali metal and transition metal doped graphene nanoribbon surface: A DFT approach
    R, Deji / Verma, Akarsh / Choudhary, B.C. / Sharma, Ramesh K. et al. | 2021

    How to get this title?

    Check access
    Download

    Download is DRM protected.

    Commercial Copyright fee: €36.00 Basic fee: €4.00 Total price: €40.00
    Academic Copyright fee: €36.00 Basic fee: €2.00 Total price: €38.00

    Export, share and cite

    Feedback