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An improved DNA-binding hot spot residues prediction method by exploring interfacial neighbor properties

Sijia Zhang, Lihua Wang, Le Zhao, Menglu Li, Mengya Liu, Ke Li, Yannan Bin, Junfeng Xia
2021 BMC Bioinformatics  
Conclusions We have developed an accurate improved prediction model, inpPDH, for hot spot residues in protein–DNA binding interfaces by given the structure of a protein–DNA complex.  ...  To improve the prediction performance, we extract hybrid features which incorporate traditional features and new interfacial neighbor properties.  ...  In this study, we developed an improved structure-based protein-DNA hot spot prediction model termed inpPDH, which integrated traditional properties used in previous hot spot prediction tasks [12] [13  ... 
doi:10.1186/s12859-020-03871-1 pmid:34000983 fatcat:3xwyu5kknra3pnosagdwhajuhm

Computationally identifying hot spots in protein-DNA binding interfaces using an ensemble approach

Yuliang Pan, Shuigeng Zhou, Jihong Guan
2020 BMC Bioinformatics  
Here, we report a new computational method for effectively predicting hot spots in protein-DNA binding interfaces.  ...  PreHots, which is based on stack ensemble of boosting algorithms, can reliably predict hot spots at the protein-DNA binding interface on a large scale.  ...  SPOT-Disorder [45] and RaporX-Property [46] were used to predict disorder regions of protein-DNA binding residues.  ... 
doi:10.1186/s12859-020-03675-3 pmid:32938375 pmcid:PMC7495898 fatcat:6tqc5nfebzdyth3g3gsolhzgqi

Hot spot prediction in protein-protein interactions by an ensemble system

Quanya Liu, Peng Chen, Bing Wang, Jun Zhang, Jinyan Li
2018 BMC Systems Biology  
In order to address the issue, many computational methods have been developed to predict hot spot residues.  ...  Hot spot residues are functional sites in protein interaction interfaces. The identification of hot spot residues is time-consuming and laborious using experimental methods.  ...  Funding The publication costs of this article was covered by the National Natural Science Foundation of China No. 61672035 and this work was also supported by the National Natural Science Foundation of  ... 
doi:10.1186/s12918-018-0665-8 pmid:30598091 pmcid:PMC6311905 fatcat:hhvxct6fzzc5hcx4dth4scux6u

Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery

Stephani Joy Y. Macalino, Shaherin Basith, Nina Abigail B. Clavio, Hyerim Chang, Soosung Kang, Sun Choi
2018 Molecules  
However, targeting PPIs are challenging due to their "undruggable" binding interfaces.  ...  Finally, we conclude by presenting the limits of in silico application in drug discovery and offer a perspective in the field of computer-aided PPI drug discovery.  ...  Prevailing ML predictors apply binary classification, where a target residue is classified as either interfacial or non-interfacial by utilizing the target features or adjacent residues to formulate predictions  ... 
doi:10.3390/molecules23081963 pmid:30082644 fatcat:e6cduopkq5gprcmwane7twfdam

PCRPi: Presaging Critical Residues in Protein interfaces, a new computational tool to chart hot spots in protein interfaces

Salam A. Assi, Tomoyuki Tanaka, Terence H. Rabbitts, Narcis Fernandez-Fuentes
2009 Nucleic Acids Research  
We have benchmarked our method using a large set of experimentally verified hot spot residues and on a blind prediction on the protein complex formed by HRAS protein and a single domain antibody.  ...  Here, we describe a new computational approach to predict hot spot residues in protein interfaces.  ...  small and complementary set of interfacial residues-a hot spot-of binding energy surrounded by weaker interactions providing specificity.  ... 
doi:10.1093/nar/gkp1158 pmid:20008102 pmcid:PMC2847225 fatcat:2fqj7qwwczhopnoz25m5hdjq5m

Heterodimer Binding Scaffolds Recognition via the Analysis of Kinetically Hot Residues

Ognjen Perišić
2018 Pharmaceuticals  
Lise et al. [66, 67] combined machine learning and energy-based methods to predict hot spot residues.  ...  The recognition of binding residues using an analysis of sequential and structural properties of heteromeric, transient protein-protein interactions produced very good overall results, as shown by Neuvirth  ...  Hui Lu for suggesting him to work on the problem of heterodimer interactions and for advising him to use the first-layer residues to boost up the prediction.  ... 
doi:10.3390/ph11010029 pmid:29547506 pmcid:PMC5874725 fatcat:53kf2dqn3ba6rhrsjwtyhn5ljy

Prediction of physical protein–protein interactions

András Szilágyi, Vera Grimm, Adrián K Arakaki, Jeffrey Skolnick
2005 Physical Biology  
For an adequate comparative evaluation of prediction and high-throughput experimental methods, an appropriately large benchmark set of biophysically characterized protein complexes would be needed, but  ...  The shortcomings of experimental techniques affect both the further development and the fair evaluation of computational prediction methods.  ...  These residues, defined by having a significant drop in the binding affinity when mutated to alanine are called 'hot spots'.  ... 
doi:10.1088/1478-3975/2/2/s01 pmid:16204844 fatcat:sslb5ps5ufbvfpbflioc27y7zm

Heterodimer binding scaffolds recognition via the analysis of kinetically hot residues [article]

Ognjen Perišić
2016 arXiv   pre-print
The results presented in this paper suggest that in heterodimers, at least one partnering chain has interacting scaffold determined by the immovable kinetically hot residues.  ...  The algorithm adjusts the number of modes used in the GNM's weighted sum calculation using the ratio of predicted and expected numbers of target residues (contact and first layer residues).  ...  Hui Lu for suggesting him to work on the problem of heterodimer interactions and for advising him to use the first layer residues to boost up the prediction.  ... 
arXiv:1609.06556v1 fatcat:rk7vlawypbcinoac5y4foawmey

Bridging protein local structures and protein functions

Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, Luonan Chen
2008 Amino Acids  
One of the major goals of molecular and evolutionary biology is to understand the functions of proteins by extracting functional information from protein sequences, structures and interactions.  ...  These methods include computational tools to identify the structural motifs and reveal the strong relationship between these pre-computed local structures and protein functions.  ...  The authors are grateful to the anonymous referees as well as editors for comments and for helping to improve the earlier version.  ... 
doi:10.1007/s00726-008-0088-8 pmid:18421562 fatcat:micrifjcrfetnafnm4fx45ouom

Analysis of Protein Protein Dimeric Interfaces

Feihong Wu, Fadi Towfic, Drena Dobbs, Vasant Honavar
2007 2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007)  
Interface residues tend to be surrounded by hydrophobic neighbors and tend to form clusters consisting of three or more interfaces residues.  ...  Preliminary results suggest the possibility of using the six the properties to identify putative interface residues.  ...  by the voting method has ≥ 4 neighbors in its surface micro-environment that are predicted to be interface residues, it is reclassified as an interface residue.  ... 
doi:10.1109/bibm.2007.60 fatcat:x7m3jwtxrvfddk57lhzmpiyjbm

PCalign: a method to quantify physicochemical similarity of protein-protein interfaces

Shanshan Cheng, Yang Zhang, Charles L Brooks
2015 BMC Bioinformatics  
This method uses an order-independent algorithm, geometric hashing, to superimpose the backbone atoms of a given pair of interfaces, and provides a normalized scoring function, PC-score, to account for  ...  We demonstrate that PCalign outperforms existing methods, and additionally facilitates comparative studies across models of different resolutions, which are not accommodated by existing methods.  ...  Acknowledgements This work was supported by NSF grant: MCB1121575.  ... 
doi:10.1186/s12859-015-0471-x pmid:25638036 pmcid:PMC4339745 fatcat:u4cp3gorvbbl7jdllk7zfaqnpy

Protein–Protein Interfaces in Viral Capsids Are Structurally Unique

Shanshan Cheng, Charles L. Brooks
2015 Journal of Molecular Biology  
Viral capsids exhibit elaborate and symmetrical architectures of defined sizes and remarkable mechanical properties not seen with cellular macromolecular complexes.  ...  Given the uniqueness of the higher order organization of viral capsid proteins in the virosphere, we explored the question of whether the patterns of protein-protein interactions within viral capsids are  ...  of a few hot spot residues anchoring protein-protein association in general).  ... 
doi:10.1016/j.jmb.2015.09.008 pmid:26375252 pmcid:PMC4624513 fatcat:na5lxq3bjbehxa4ewqfbdcxxxy

Biophysical characterization of the ETV6 PNT domain polymerization interfaces

Chloe A.N. Gerak, Sophia Y. Cho, Maxim Kolesnikov, Mark Okon, Michael E.P. Murphy, Richard B. Sessions, Michel Roberge, Lawrence P. McIntosh
2021 Journal of Biological Chemistry  
ETV6 is an ETS family transcriptional repressor that self-associates by its PNT domain to facilitate cooperative DNA binding.  ...  Surface plasmon resonance-monitored alanine scanning mutagenesis studies identified hot spot regions within the self-association interfaces.  ...  In principle, one could modify an ETV6 PNT domain residue, that does not affect binding and is near a hot spot, to a cysteine for this approach.  ... 
doi:10.1016/j.jbc.2021.100284 pmid:33450226 pmcid:PMC7949025 fatcat:f6gcirb3qbe75msiggnd6blwpm

Biophysical characterization of the ETV6 PNT domain polymerization interfaces [article]

Chloe A. N. Gerak, Sophia Y. Cho, Maxim Kolesnikov, Mark Okon, Michael E. P. Murphy, Richard B. Sessions, Michel Roberge, Lawrence P. McIntosh
2020 biorxiv/medrxiv   pre-print
ETV6 is an ETS family transcriptional repressor that self-associates by its PNT domain to facilitate cooperative DNA binding.  ...  Amide hydrogen exchange and surface plasmon resonance-monitored alanine scanning mutagenesis studies identified hot spot regions within the self-association interfaces.  ...  In principle, one could modify an ETV6 PNT domain residue, that does not affect binding and is near a hot spot, to a cysteine for this approach.  ... 
doi:10.1101/2020.08.21.262121 fatcat:3647uxytubfptiln7sktsdv6pa

Computer-aided design of functional protein interactions

Daniel J Mandell, Tanja Kortemme
2009 Nature Chemical Biology  
Predictive methods for the computational design of proteins search for amino acid sequences adopting desired structures that perform specific functions.  ...  Typically, design of 'function' is formulated as engineering new and altered binding activities into proteins.  ...  This work was supported by a CAREER award from the US National Science Foundation (T.K.) and a PhRMA Foundation Predoctoral Fellowship (D.J.M.).  ... 
doi:10.1038/nchembio.251 pmid:19841629 fatcat:mhi7ajt6effchiwvb6ffqcelhm
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