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Protein interface predictor

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https://www.readbyqxmd.com/read/27792167/predicting-protein-protein-interaction-sites-using-sequence-descriptors-and-site-propensity-of-neighboring-amino-acids
#1
Tzu-Hao Kuo, Kuo-Bin Li
Information about the interface sites of Protein-Protein Interactions (PPIs) is useful for many biological research works. However, despite the advancement of experimental techniques, the identification of PPI sites still remains as a challenging task. Using a statistical learning technique, we proposed a computational tool for predicting PPI interaction sites. As an alternative to similar approaches requiring structural information, the proposed method takes all of the input from protein sequences. In addition to typical sequence features, our method takes into consideration that interaction sites are not randomly distributed over the protein sequence...
October 26, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27667482/modeling-oblong-proteins-and-water-mediated-interfaces-with-rosettadock-in-capri-rounds-28-35
#2
Nicholas A Marze, Jeliazko R Jeliazkov, Shourya Sonkar Roy Burman, Scott E Boyken, Frank DiMaio, Jeffrey J Gray
The 28th-35th rounds of the Critical Assessment of PRotein Interactions (CAPRI) served as a practical benchmark for our RosettaDock protein-protein docking protocols, highlighting strengths and weaknesses of the approach. We achieved acceptable or better quality models in three out of 11 targets. For the two α-repeat protein-green fluorescent protein (αrep-GFP) complexes, we used a novel ellipsoidal partial-global docking method (Ellipsoidal Dock) to generate models with 2.2 Å/1.5 Å interface RMSD, capturing 49%/42% of the native contacts, for the 7-/5-repeat αrep complexes...
September 26, 2016: Proteins
https://www.readbyqxmd.com/read/27383535/fastrnabindr-fast-and-accurate-prediction-of-protein-rna-interface-residues
#3
Yasser El-Manzalawy, Mostafa Abbas, Qutaibah Malluhi, Vasant Honavar
A wide range of biological processes, including regulation of gene expression, protein synthesis, and replication and assembly of many viruses are mediated by RNA-protein interactions. However, experimental determination of the structures of protein-RNA complexes is expensive and technically challenging. Hence, a number of computational tools have been developed for predicting protein-RNA interfaces. Some of the state-of-the-art protein-RNA interface predictors rely on position-specific scoring matrix (PSSM)-based encoding of the protein sequences...
2016: PloS One
https://www.readbyqxmd.com/read/27378293/metapred2cs-a-sequence-based-meta-predictor-for-protein-protein-interactions-of-prokaryotic-two-component-system-proteins
#4
Altan Kara, Martin Vickers, Martin Swain, David E Whitworth, Narcis Fernandez-Fuentes
MOTIVATION: Two-component systems (TCS) are the main signalling pathways of prokaryotes, and control a wide range of biological phenomena. Their functioning depends on interactions between TCS proteins, the specificity of which is poorly understood. RESULTS: The MetaPred2CS web-server interfaces a sequence-based meta-predictor specifically designed to predict pairing of the histidine kinase and response-regulator proteins forming TCSs. MetaPred2CS integrates six sequence-based methods using a support vector machine classifier and has been intensively tested under different benchmarking conditions: (i) species specific gene sets; (ii) neighbouring versus orphan pairs; and (iii) k-fold cross validation on experimentally validated datasets...
July 4, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27378157/chronic-impedance-spectroscopy-of-an-endovascular-stent-electrode-array
#5
Nicholas L Opie, Sam E John, Gil S Rind, Stephen M Ronayne, David B Grayden, Anthony N Burkitt, Clive N May, Terence J O'Brien, Thomas J Oxley
OBJECTIVE: Recently, we reported a minimally invasive stent-electrode array capable of recording neural signals from within a blood vessel. We now investigate the use of electrochemical impedance spectroscopy (EIS) measurements to infer changes occurring to the electrode-tissue interface from devices implanted in a cohort of sheep for up to 190 days. APPROACH: In a cohort of 15 sheep, endovascular stent-electrode arrays were implanted in the superior sagittal sinus overlying the motor cortex for up to 190 days...
August 2016: Journal of Neural Engineering
https://www.readbyqxmd.com/read/27303709/sstar-a-stand-alone-easy-to-use-antimicrobial-resistance-gene-predictor
#6
Tom J B de Man, Brandi M Limbago
We present the easy-to-use Sequence Search Tool for Antimicrobial Resistance, SSTAR. It combines a locally executed BLASTN search against a customizable database with an intuitive graphical user interface for identifying antimicrobial resistance (AR) genes from genomic data. Although the database is initially populated from a public repository of acquired resistance determinants (i.e., ARG-ANNOT), it can be customized for particular pathogen groups and resistance mechanisms. For instance, outer membrane porin sequences associated with carbapenem resistance phenotypes can be added, and known intrinsic mechanisms can be included...
January 2016: MSphere
https://www.readbyqxmd.com/read/27284087/exploring-the-interplay-between-experimental-methods-and-the-performance-of-predictors-of-binding-affinity-change-upon-mutations-in-protein-complexes
#7
Cunliang Geng, Anna Vangone, Alexandre M J J Bonvin
Reliable prediction of binding affinity changes (ΔΔG) upon mutations in protein complexes relies not only on the performance of computational methods but also on the availability and quality of experimental data. Binding affinity changes can be measured by various experimental methods with different accuracies and limitations. To understand the impact of these on the prediction of binding affinity change, we present the Database of binding Affinity Change Upon Mutation (DACUM), a database of 1872 binding affinity changes upon single-point mutations, a subset of the SKEMPI database (Moal,I...
August 2016: Protein Engineering, Design & Selection: PEDS
https://www.readbyqxmd.com/read/27224906/predictsnp2-a-unified-platform-for-accurately-evaluating-snp-effects-by-exploiting-the-different-characteristics-of-variants-in-distinct-genomic-regions
#8
Jaroslav Bendl, Miloš Musil, Jan Štourač, Jaroslav Zendulka, Jiří Damborský, Jan Brezovský
An important message taken from human genome sequencing projects is that the human population exhibits approximately 99.9% genetic similarity. Variations in the remaining parts of the genome determine our identity, trace our history and reveal our heritage. The precise delineation of phenotypically causal variants plays a key role in providing accurate personalized diagnosis, prognosis, and treatment of inherited diseases. Several computational methods for achieving such delineation have been reported recently...
May 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/26851400/software-tools-for-simultaneous-data-visualization-and-t-cell-epitopes-and-disorder-prediction-in-proteins
#9
Davorka R Jandrlić, Goran M Lazić, Nenad S Mitić, Mirjana D Pavlović
We have developed EpDis and MassPred, extendable open source software tools that support bioinformatic research and enable parallel use of different methods for the prediction of T cell epitopes, disorder and disordered binding regions and hydropathy calculation. These tools offer a semi-automated installation of chosen sets of external predictors and an interface allowing for easy application of the prediction methods, which can be applied either to individual proteins or to datasets of a large number of proteins...
April 2016: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/26507825/the-cancer-genome-atlas-clinical-explorer-a-web-and-mobile-interface-for-identifying-clinical-genomic-driver-associations
#10
HoJoon Lee, Jennifer Palm, Susan M Grimes, Hanlee P Ji
BACKGROUND: The Cancer Genome Atlas (TCGA) project has generated genomic data sets covering over 20 malignancies. These data provide valuable insights into the underlying genetic and genomic basis of cancer. However, exploring the relationship among TCGA genomic results and clinical phenotype remains a challenge, particularly for individuals lacking formal bioinformatics training. Overcoming this hurdle is an important step toward the wider clinical translation of cancer genomic/proteomic data and implementation of precision cancer medicine...
October 27, 2015: Genome Medicine
https://www.readbyqxmd.com/read/26506533/predicting-the-effect-of-mutations-on-protein-protein-binding-interactions-through-structure-based-interface-profiles
#11
Jeffrey R Brender, Yang Zhang
The formation of protein-protein complexes is essential for proteins to perform their physiological functions in the cell. Mutations that prevent the proper formation of the correct complexes can have serious consequences for the associated cellular processes. Since experimental determination of protein-protein binding affinity remains difficult when performed on a large scale, computational methods for predicting the consequences of mutations on binding affinity are highly desirable. We show that a scoring function based on interface structure profiles collected from analogous protein-protein interactions in the PDB is a powerful predictor of protein binding affinity changes upon mutation...
October 2015: PLoS Computational Biology
https://www.readbyqxmd.com/read/26460190/computational-prediction-of-protein-interfaces-a-review-of-data-driven-methods
#12
REVIEW
Li C Xue, Drena Dobbs, Alexandre M J J Bonvin, Vasant Honavar
Reliably pinpointing which specific amino acid residues form the interface(s) between a protein and its binding partner(s) is critical for understanding the structural and physicochemical determinants of protein recognition and binding affinity, and has wide applications in modeling and validating protein interactions predicted by high-throughput methods, in engineering proteins, and in prioritizing drug targets. Here, we review the basic concepts, principles and recent advances in computational approaches to the analysis and prediction of protein-protein interfaces...
November 30, 2015: FEBS Letters
https://www.readbyqxmd.com/read/26418056/human-papillomavirus-genome-wide-identification-of-t-cell-epitopes-for-peptide-vaccine-development-against-cervical-cancer-an-integration-of-computational-analysis-and-experimental-assay
#13
Bo Li, Xianfang Zheng, Chuancui Hu, Yunxia Cao
Human papillomavirus (HPV) has long been documented as the primary factor causing cervical cancer and other complications, and development of immunotherapeutic vaccines against HPV is thought to be an important approach in preventing women from HPV infections. It is known that the first step in vaccine development is to find potent T-cell epitopes in HPV proteins that can be effectively recognized and presented by the human leukocyte antigen (HLA) system. In the current study, we proposed a synthetic pipeline that integrates computational analysis and experimental assay to discover new peptide epitopes from HPV genome with high affinity to the HLA-A*0201, one of the most frequent HLA allele in Caucasian and Asian populations...
October 2015: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/26244771/role-of-gxxxg-motifs-in-transmembrane-domain-interactions
#14
REVIEW
Mark G Teese, Dieter Langosch
Transmembrane (TM) helices of integral membrane proteins can facilitate strong and specific noncovalent protein-protein interactions. Mutagenesis and structural analyses have revealed numerous examples in which the interaction between TM helices of single-pass membrane proteins is dependent on a GxxxG or (small)xxx(small) motif. It is therefore tempting to use the presence of these simple motifs as an indicator of TM helix interactions. In this Current Topic review, we point out that these motifs are quite common, with more than 50% of single-pass TM domains containing a (small)xxx(small) motif...
August 25, 2015: Biochemistry
https://www.readbyqxmd.com/read/26198590/predicting-the-agitation-induced-aggregation-of-monoclonal-antibodies-using-surface-tensiometry
#15
Ian C Shieh, Ankit R Patel
Adsorption of antibody therapeutics to air-liquid interfaces can enhance aggregation, particularly when the solution does not contain protective surfactant or when the surfactant is diluted as occurs during preparation of intravenous infusion bags. The ability to predict an antibody's propensity for interfacially mediated aggregation is particularly useful during product development to ensure the quality, potency, and safety of the therapeutic. To develop a predictive tool, we investigated the surface pressure and surface excess of a panel of 16 antibodies as well as determined their aggregation propensity at the air-liquid interface in an agitation stress model...
September 8, 2015: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/26142185/jassa-a-comprehensive-tool-for-prediction-of-sumoylation-sites-and-sims
#16
Guillaume Beauclair, Antoine Bridier-Nahmias, Jean-François Zagury, Ali Saïb, Alessia Zamborlini
MOTIVATION: Post-translational modification by the Small Ubiquitin-like Modifier (SUMO) proteins, a process termed SUMOylation, is involved in many fundamental cellular processes. SUMO proteins are conjugated to a protein substrate, creating an interface for the recruitment of cofactors harboring SUMO-interacting motifs (SIMs). Mapping both SUMO-conjugation sites and SIMs is required to study the functional consequence of SUMOylation. To define the best candidate sites for experimental validation we designed JASSA, a Joint Analyzer of SUMOylation site and SIMs...
November 1, 2015: Bioinformatics
https://www.readbyqxmd.com/read/26061299/structure-based-rational-design-of-peptide-hydroxamic-acid-inhibitors-to-target-tumor-necrosis-factor-%C3%AE-converting-enzyme-as-potential-therapeutics-for-hepatitis
#17
Dan Wu, Qiuhong Gu, Ning Zhao, Fei Xia, Zhiwei Li
The human tumor necrosis factor-α converting enzyme (TACE) has recently been raised as a new and promising therapeutic target of hepatitis and other inflammatory diseases. Here, we reported a successful application of the solved crystal structure of TACE complex with a peptide-like ligand INN for rational design of novel peptide hydroxamic acid inhibitors with high potency and selectivity to target and inhibit TACE. First, the intermolecular interactions between TACE catalytic domain and INN were characterized through an integrated bioinformatics approach, with which the key substructures of INN that dominate ligand binding were identified...
December 2015: Journal of Drug Targeting
https://www.readbyqxmd.com/read/25982853/protdcal-a-program-to-compute-general-purpose-numerical-descriptors-for-sequences-and-3d-structures-of-proteins
#18
Yasser B Ruiz-Blanco, Waldo Paz, James Green, Yovani Marrero-Ponce
BACKGROUND: The exponential growth of protein structural and sequence databases is enabling multifaceted approaches to understanding the long sought sequence-structure-function relationship. Advances in computation now make it possible to apply well-established data mining and pattern recognition techniques to these data to learn models that effectively relate structure and function. However, extracting meaningful numerical descriptors of protein sequence and structure is a key issue that requires an efficient and widely available solution...
May 16, 2015: BMC Bioinformatics
https://www.readbyqxmd.com/read/25970262/chseq-a-database-of-chameleon-sequences
#19
REVIEW
Wenlin Li, Lisa N Kinch, P Andrew Karplus, Nick V Grishin
Chameleon sequences (ChSeqs) refer to sequence strings of identical amino acids that can adopt different conformations in protein structures. Researchers have detected and studied ChSeqs to understand the interplay between local and global interactions in protein structure formation. The different secondary structures adopted by one ChSeq challenge sequence-based secondary structure predictors. With increasing numbers of available Protein Data Bank structures, we here identify a large set of ChSeqs ranging from 6 to 10 residues in length...
July 2015: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/25819671/outlier-detection-at-the-transcriptome-proteome-interface
#20
Yawwani Gunawardana, Shuhei Fujiwara, Akiko Takeda, Jeongmin Woo, Christopher Woelk, Mahesan Niranjan
BACKGROUND: In high-throughput experimental biology, it is widely acknowledged that while expression levels measured at the levels of transcriptome and the corresponding proteome do not, in general, correlate well, messenger RNA levels are used as convenient proxies for protein levels. Our interest is in developing data-driven computational models that can bridge the gap between these two levels of measurement at which different mechanisms of regulation may act on different molecular species causing any observed lack of correlations...
August 1, 2015: Bioinformatics
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