Computational characterization and design of SARS coronavirus receptor recognition and antibody neutralization.

Abstract:

:The sequential determination of crystal structures of the SARS coronavirus spike receptor-binding domain (RBD) in complex with its cellular receptor or neutralizing antibody opened a door for the design and development of antiviral competitive inhibitors. Based on those complex structures, we conduct computational characterization and design of RBD-mediated receptor recognition and antibody neutralization. The comparisons between computational predictions and experimental evidences validate our structural bioinformatics protocols. And the calculations predict a number of single substitutions on RBD, receptor or antibody that could remarkably elevate the binding affinities of those complexes. It is reasonable to anticipate our structure-based computation-derived hypotheses could be informative to the future biochemical and immunological tests.

journal_name

Comput Biol Chem

authors

Zhang Y,Zheng N,Zhong Y

doi

10.1016/j.compbiolchem.2007.02.005

subject

Has Abstract

pub_date

2007-04-01 00:00:00

pages

129-33

issue

2

eissn

1476-9271

issn

1476-928X

pii

S1476-9271(07)00026-6

journal_volume

31

pub_type

杂志文章
  • C3: An R package for cross-species compendium-based cell-type identification.

    abstract::Cell type identification from an unknown sample can often be done by comparing its gene expression profile against a gene expression database containing profiles of a large number of cell-types. This type of compendium-based cell-type identification strategy is particularly successful for human and mouse samples becau...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2018.10.003

    authors: Kabir MH,Djordjevic D,O'Connor MD,Ho JWK

    更新日期:2018-12-01 00:00:00

  • Predicting microRNA biological functions based on genes discriminant analysis.

    abstract::Although thousands of microRNAs (miRNAs) have been identified in recent experimental efforts, it remains a challenge to explore their specific biological functions through molecular biological experiments. Since those members from same family share same or similar biological functions, classifying new miRNAs into thei...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2017.09.008

    authors: Ding T,Xu J,Sun M,Zhu S,Gao J

    更新日期:2017-12-01 00:00:00

  • Phosphorylation mapping of laminin α1-chain: Kinases in association with active sites.

    abstract::Laminin-111 is a trimeric glycoprotein of the extracellular matrix (ECM) that holds a significant role in cell adhesion, migration and differentiation. Laminin-111 is the most studied laminin isoform, composed of three chains; α1, β1 and γ1. Phosphorylation is the most common eukaryotic post - translational modificati...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2019.04.012

    authors: Galliou PA,Verrou KM,Koliakos G

    更新日期:2019-06-01 00:00:00

  • Identification of possible siRNA molecules for TDP43 mutants causing amyotrophic lateral sclerosis: In silico design and molecular dynamics study.

    abstract::The DNA binding protein, TDP43 is a major protein involved in amyotrophic lateral sclerosis and other neurological disorders such as frontotemporal dementia, Alzheimer disease, etc. In the present study, we have designed possible siRNAs for the glycine rich region of tardbp mutants causing ALS disorder based on a syst...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2016.01.001

    authors: Bhandare VV,Ramaswamy A

    更新日期:2016-04-01 00:00:00

  • A Computational workflow for the identification of the potent inhibitor of type II secretion system traffic ATPase of Pseudomonas aeruginosa.

    abstract::Bacterial type II secretion system has now become an attractive target for antivirulence drug development. The aim of the present study was to characterize the binding site of the type II secretion system traffic ATPase GspER of Pseudomonas aeruginosa, and identify potent inhibitors using extensive computational and v...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2018.07.012

    authors: Arifuzzaman M,Mitra S,Jahan SI,Jakaria M,Abeda T,Absar N,Dash R

    更新日期:2018-10-01 00:00:00

  • The aspartate aminotransferase-like domain of Firmicutes MocR transcriptional regulators.

    abstract::Bacterial MocR transcriptional regulators possess an N-terminal DNA-binding domain containing a conserved helix-turn-helix module and an effector-binding and/or oligomerization domain at the C-terminus, homologous to fold type-I pyridoxal 5'-phosphate (PLP) enzymes. Since a comprehensive structural analysis of the Moc...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2015.05.003

    authors: Milano T,Contestabile R,Lo Presti A,Ciccozzi M,Pascarella S

    更新日期:2015-10-01 00:00:00

  • From NGS assembly challenges to instability of fungal mitochondrial genomes: A case study in genome complexity.

    abstract::The presence of repetitive or non-unique DNA persisting over sizable regions of a eukaryotic genome can hinder the genome's successful de novo assembly from short reads: ambiguities in assigning genome locations to the non-unique subsequences can result in premature termination of contigs and thus overfragmented assem...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2016.02.016

    authors: Misas E,Muñoz JF,Gallo JE,McEwen JG,Clay OK

    更新日期:2016-04-01 00:00:00

  • FSDB: a frameshift signal database.

    abstract::Programmed frameshifting is a recoding event in which a ribosome shifts reading frame by one or more nucleotides at a specific mRNA signal between overlapping genes. Programmed frameshifting is involved in the expression of many genes in a wide range of organisms, especially in viruses and bacteria. The mechanism of p...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2007.05.004

    authors: Moon S,Byun Y,Han K

    更新日期:2007-08-01 00:00:00

  • Multi-group cancer outlier differential gene expression detection.

    abstract::It has recently been shown that cancer genes (oncogenes) tend to have heterogeneous expressions across disease samples. So it is reasonable to assume that in a microarray data only a subset of disease samples will be activated (often referred to as outliers), which presents some new challenges for statistical analysis...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2007.02.004

    authors: Liu F,Wu B

    更新日期:2007-04-01 00:00:00

  • Genome-wide identification and expression analysis of SWI1 genes in Boechera species.

    abstract::As a mode of reproduction in plants, apomixis leads to the generation of clones via seeds. Apomictic plants form viable diploid female gametes without meiosis (apomeiosis) and produce embryos without fertilization (parthenogenesis). Apomeiosis, as a major component of apomixis, has recently been reported in some Arabi...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2016.04.004

    authors: Sezer F,Yüzbaşioğlu G,Özbilen A,Taşkin KM

    更新日期:2016-06-01 00:00:00

  • Disruption of murine Tcte3-3 induces tissue specific apoptosis via co-expression of Anxa5 and Pebp1.

    abstract::Programmed cell death or apoptosis plays a vital physiological role in the development and homeostasis. Any discrepancy in apoptosis may trigger testicular and neurodegenerative diseases, ischemic damage, autoimmune disorders and many types of cancer. Tcte3 (T-complex testis expressed 3) is an accessory component of a...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2014.10.005

    authors: Parveen Z,Bibi Z,Bibi N,Neesen J,Rashid S

    更新日期:2014-12-01 00:00:00

  • The anesthetic action of some polyhalogenated ethers-Monte Carlo method based QSAR study.

    abstract::Up to this date, there has been an ongoing debate about the mode of action of general anesthetics, which have postulated many biological sites as targets for their action. However, postoperative nausea and vomiting are common problems in which inhalational agents may have a role in their development. When a mode of ac...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2018.04.009

    authors: Golubović M,Lazarević M,Zlatanović D,Krtinić D,Stoičkov V,Mladenović B,Milić DJ,Sokolović D,Veselinović AM

    更新日期:2018-08-01 00:00:00

  • Novel 2,4-disubstituted quinazolines as cytotoxic agents and JAK2 inhibitors: Synthesis, in vitro evaluation and molecular dynamics studies.

    abstract::Recent studies reported the involvement of JAK2/STAT3 pathway in various solid tumours including breast, ovarian, prostate and lung cancers. Clinical literature also reported the lowered burden in breast and ovarian cancers by targeting JAK2 pathway. In this study, a series of novel 2,4-disubstituted quinazolines (2a-...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2019.01.008

    authors: Jyothi Buggana S,Paturi MC,Perka H,Gade DR,Vvs RP

    更新日期:2019-04-01 00:00:00

  • Computational analysis for the determination of deleterious nsSNPs in human MTHFR gene.

    abstract::Methylenetetrahydrofolate reductase (MTHFR) is a key enzyme involved in folate metabolism and plays a central role in DNA methylation and biosynthesis. MTHFR mutations may alter the cellular folate supply which in turn affects nucleic acid synthesis, DNA methylation and chromosomal damage. The identification of number...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2018.02.022

    authors: Desai M,Chauhan JB

    更新日期:2018-06-01 00:00:00

  • The binding mode of picrotoxinin in GABAA-ρ receptors: Insight into the subunit's selectivity in the transmembrane domain.

    abstract::The channel blocker picrotoxinin has been studied with GABAA-ρ1 and GABAA-ρ2 homology models based on the GluCl crystal structure. Picrotoxinin is tenfold more potent for GABAA-ρ2 than for GABAA-ρ1 homomeric channels. This intra-subunit selectivity arises from the unconserved residues at the 2' sites, which are the es...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2016.07.003

    authors: Naffaa MM,Samad A

    更新日期:2016-10-01 00:00:00

  • Putative dual inhibitors of Janus kinase 1 and 3 (JAK1/3): Pharmacophore based hierarchical virtual screening.

    abstract::Janus kinase 1 and 3 are non-receptor protein tyrosine kinases, involved in the regulation of various cytokines implicated in the pathogenesis of autoimmune and inflammatory disease conditions. Thus, they serve as therapeutic targets for the designing of multi-targeted agents for the treatment of inflammatory-mediated...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2018.07.009

    authors: Jasuja H,Chadha N,Singh PK,Kaur M,Bahia MS,Silakari O

    更新日期:2018-10-01 00:00:00

  • Effects of DNA secondary structure on oligonucleotide probe binding efficiency.

    abstract::Secondary structure motifs in nucleic acid probes generally impair intended hybridization reactions and so efforts to predict and avoid such structures are commonly employed in probe design schemes. Another key facet of probe design that has received much less attention, however, is that secondary structure at targete...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2005.09.002

    authors: Koehler RT,Peyret N

    更新日期:2005-12-01 00:00:00

  • Complex phylogenetic profiling reveals fundamental genotype-phenotype associations.

    abstract::We have developed a computational technique refereed to as complex phylogenetic profiling. Our approach combines logic analyses of gene phylogenetic profiles and phenotype data. Logic analysis of phylogenetic profiles identifies sets of proteins whose presence or absence follows certain logic relationships. Our approa...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2008.07.003

    authors: Antonov AV,Mewes HW

    更新日期:2008-12-01 00:00:00

  • Chromatographic and computational screening of anisotropic lipophilicity and pharmacokinetics of newly synthesized 1-aryl-3-ethyl-3-methylsuccinimides.

    abstract::The present study is focused on a series of newly synthesized 1-aryl-3-ethyl-3-methylsuccinimide derivatives, as potential anticonvulsants. The retention behavior of eleven succinimide derivatives was determined by using reversed phase high performance liquid chromatography (RP-HPLC) and reversed phase high performanc...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2019.107161

    authors: Kovačević S,Banjac MK,Podunavac-Kuzmanović S,Milošević N,Ćurčić J,Vulić J,Šeregelj V,Banjac N,Ušćumlić G

    更新日期:2020-02-01 00:00:00

  • A class imbalance-aware Relief algorithm for the classification of tumors using microarray gene expression data.

    abstract::DNA microarray data has been widely used in cancer research due to the significant advantage helped to successfully distinguish between tumor classes. However, typical gene expression data usually presents a high-dimensional imbalanced characteristic, which poses severe challenge for traditional machine learning metho...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2019.03.017

    authors: He Y,Zhou J,Lin Y,Zhu T

    更新日期:2019-06-01 00:00:00

  • Automated prediction of three-way junction topological families in RNA secondary structures.

    abstract::We present an algorithm for automatically predicting the topological family of any RNA three-way junction, given only the information from the secondary structure: the sequence and the Watson-Crick pairings. The parameters of the algorithm have been determined on a data set of 33 three-way junctions whose 3D conformat...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2011.11.001

    authors: Lamiable A,Barth D,Denise A,Quessette F,Vial S,Westhof E

    更新日期:2012-04-01 00:00:00

  • Functional and structural insights into novel DREB1A transcription factors in common wheat (Triticum aestivum L.): A molecular modeling approach.

    abstract::Triticum aestivum L. known as common wheat is one of the most important cereal crops feeding a large and growing population. Various environmental stress factors including drought, high salinity and heat etc. adversely affect wheat production in a significant manner. Dehydration-responsive element-binding (DREB1A) fac...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2016.07.008

    authors: Kumar A,Kumar S,Kumar U,Suravajhala P,Gajula MN

    更新日期:2016-10-01 00:00:00

  • Markovian encoding models in human splice site recognition using SVM.

    abstract::Splice site recognition is among the most significant and challenging tasks in bioinformatics due to its key role in gene annotation. Effective prediction of splice site requires nucleotide encoding methods that reveal the characteristics of DNA sequences to provide appropriate features to serve as input of machine le...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2018.02.005

    authors: Pashaei E,Aydin N

    更新日期:2018-04-01 00:00:00

  • Statistical models in assessing fold change of gene expression in real-time RT-PCR experiments.

    abstract::Real-time RT-PCR has been frequently used in quantitative research in molecular biology and bioinformatics. It provides remarkably useful technology to assess expression of genes. Although mathematical models for gene amplification process have been studied, statistical models and methods for data analysis in real-tim...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2005.10.005

    authors: Fu WJ,Hu J,Spencer T,Carroll R,Wu G

    更新日期:2006-02-01 00:00:00

  • New insights on gene regulation in archaea.

    abstract::Archaea represent an important and vast domain of life. This cellular domain includes a large diversity of organisms characterized as prokaryotes with basal transcriptional machinery similar to eukarya. In this work we explore the most recent findings concerning the transcriptional regulatory organization in archaeal ...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章,评审

    doi:10.1016/j.compbiolchem.2011.10.006

    authors: Tenorio-Salgado S,Huerta-Saquero A,Perez-Rueda E

    更新日期:2011-12-14 00:00:00

  • Potential protein biomarkers for systemic lupus erythematosus determined by bioinformatics analysis.

    abstract::Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disorder, and its pathogenesis in males and in cases without accompanying lupus nephritis (LN-) is not fully understood. In this study, we identified 90 (82 up- and 8 downregulated) differentially expressed genes (DEGs) common to female LN-, female LN+ a...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2019.107135

    authors: Kong J,Li L,Zhimin L,Yan J,Ji D,Chen Y,Yuanyuan W,Chen X,Shao H,Wang J,Da Z

    更新日期:2019-12-01 00:00:00

  • Carboxylic acid derivatives display potential selectivity for human histone deacetylase 6: Structure-based virtual screening, molecular docking and dynamics simulation studies.

    abstract::Human histone deacetylase 6 (HDAC6) has been shown to play a major role in oncogenic cell transformation via deacetylation of α-tubulin, making it a viable target of anticancer drug design and development. The crystal structure of HDAC6 catalytic domain 2 has been recently made available, providing avenues for structu...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2018.05.004

    authors: Uba AI,Yelekçi K

    更新日期:2018-08-01 00:00:00

  • Theoretical studies and NMR assay of coumarins and neoflavanones derivatives as potential inhibitors of acetylcholinesterase.

    abstract::Currently Alzheimer's disease (AD) is a devastating neurological disorder that mainly affects the elderly. The treatment of AD has as main objective to increase the levels of ACh in the synaptic cleft by inhibiting the cholinesterase enzymes, which are responsible for the degradation of ACh. Twenty one synthesized cou...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2020.107293

    authors: de Souza LG,Moraes PF,Leão RAC,Costa PRR,Soares RO,Pascutti PG,Figueroa-Villar JD,Rennó MN

    更新日期:2020-05-29 00:00:00

  • Principles of rapid polymerase chain reactions: mathematical modeling and experimental verification.

    abstract::Polymerase chain reaction (PCR) is an important diagnostic tool for the amplification of DNA. The PCR process can be treated as a problem in biochemical engineering. This study focuses on the development of a mathematical model of the polymerase chain reaction. The PCR process consists of three steps: denaturation of ...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2004.03.001

    authors: Whitney SE,Sudhir A,Nelson RM,Viljoen HJ

    更新日期:2004-07-01 00:00:00

  • Generating SNP barcode to evaluate SNP-SNP interaction of disease by particle swarm optimization.

    abstract::Genome-wide association analysis involved many single-nucleotide polymorphisms (SNPs) data is challenging mathematically and computationally. Hence, we propose the odds ratio-based discrete binary particle swarm optimization (OR-DBPSO) method that uses the OR as a new quantitative measure of disease risk among many SN...

    journal_title:Computational biology and chemistry

    pub_type: 杂志文章

    doi:10.1016/j.compbiolchem.2008.07.029

    authors: Chang HW,Yang CH,Ho CH,Wen CH,Chuang LY

    更新日期:2009-02-01 00:00:00