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ISSN 1386-6338 (P)
ISSN 1434-3207 (E)
In Silico Biology is a scientific research journal for the advancement of computational models and simulations applied to complex biological phenomena. We publish peer-reviewed leading-edge biological, biomedical and biotechnological research in which computer-based (i.e.,
) modeling and analysis tools are developed and utilized to predict and elucidate dynamics of biological systems, their design and control, and their evolution. Experimental support may also be provided to support the computational analyses.
In Silico Biology aims to advance the knowledge of the principles of organization of living systems. We strive to provide computational frameworks for understanding how observable biological properties arise from complex systems. In particular, we seek for integrative formalisms to decipher cross-talks underlying systems level properties, ultimate aim of multi-scale models.
Studies published in
In Silico Biology generally use theoretical models and computational analysis to gain quantitative insights into regulatory processes and networks, cell physiology and morphology, tissue dynamics and organ systems. Special areas of interest include signal transduction and information processing, gene expression and gene regulatory networks, metabolism, proliferation, differentiation and morphogenesis, among others, and the use of multi-scale modeling to connect molecular and cellular systems to the level of organisms and populations.
In Silico Biology also publishes foundational research in which novel algorithms are developed to facilitate modeling and simulations. Such research must demonstrate application to a concrete biological problem.
In Silico Biology frequently publishes special issues on seminal topics and trends. Special issues are handled by Special Issue Editors appointed by the Editor-in-Chief. Proposals for special issues should be sent to the Editor-in-Chief.
About In Silico Biology
is a pendant to
(in the living system) and
(in the test tube) biological experiments, and implies the gain of insights by computer-based simulations and model analyses.
In Silico Biology (ISB) was founded in 1998 as a purely online journal. IOS Press became the publisher of the printed journal shortly after. Today, ISB is dedicated exclusively to biological systems modeling and multi-scale simulations and is published solely by IOS Press. The previous online publisher, Bioinformation Systems, maintains a website containing studies published between 1998 and 2010 for archival purposes.
We strongly support open communications and encourage researchers to share results and preliminary data with the community. Therefore, results and preliminary data made public through conference presentations, conference proceeding or posting of unrefereed manuscripts on preprint servers will not prohibit publication in ISB. However, authors are required to modify a preprint to include the journal reference (including DOI), and a link to the published article on the ISB website upon publication.
Abstract: MicroRNAs (miRNAs) are endogenous 21–23 nucleotide molecules that are known to regulate about 30% of protein-coding genes through the RNAi pathway. Low level expression of some miRNA has limited their in-situ discovery. Such limitations could be ameliorated by in-silico methodologies. The efficacies of three major programs (ERPIN, ProMir and miR-abela) in detecting known pre-miRNA were evaluated using chicken pre-miRNA data. The sensitivity of ProMir, miR-abela and ERPIN were 53%, 57% and 93%,…respectively. The specificity of the three algorithms using 5,000 random sequences was 98.94%, 99.46%, and 99.10% for ProMir-g, ERPIN and miR-abela, respectively. The sensitivities of the existing programs are low for chicken data and an efficient algorithm may be needed to predict novel chicken pre-miRNAs.
Abstract: Albeit the great number of microarray data available on breast cancer, reliable identification of genes associated with breast cancer development remains a challenge. The aim of this work was to develop a novel method of meta-analysis for the identification of differentially expressed genes integrating results of several independent microarray experiments. We developed a statistical method for identification of up- and down-regulated genes to perform meta-analysis. The method takes advantage of hypergeometric and binomial distributions.…Using our method we performed meta-analysis of five data sets from independent cDNA-microarray experiments on breast cancer. The meta-analysis revealed that 3.2% and 2.8% of the 24,726 analyzed genes are significantly (P-value < 0.01) down- and up-regulated, respectively. We also show that properly applied meta-analysis is a good tool for comparison of different breast cancer subtypes. Our meta-analysis showed that the expression of the majority of genes does not show significant differences in different subtypes of breast cancer. Here, we report the rationale, development and application of meta-analysis that enable us to identify biologically meaningful features of breast cancer. The algorithm we propose for the meta-analysis can reveal the features specific to the breast cancer subtypes and those common to breast cancer. The results allow us to revise the previously generated lists of genes associated with breast cancer and also identify most promising anticancer drug-target genes.
Keywords: Breast cancer, cDNA microarray data, meta-analysis, differentially expressed genes, drug targets, Cyclonet database, hypergeometric distribution
Abstract: Nucleotide sequences of catalase were obtained following amplification using specific primers and were blasted against Musa acuminata catalase 2 mRNA from NCBI (157418810). Clustering of the amino acid sequences from NCBI was done using Clustal X. The latter revealed that FHIA18 catalase is more related to Ravenala madagascariensis (Musa relative) catalase while the Williams catalase is more related to a clade containing a Musa acuminata (Musa ancestor) catalase from NCBI. The tertiary…structures and the catalase consensus functional sites, based on the Pseudomonas syringae catalase structural template, were obtained for FHIA18, Williams, Ravenala madagascariensis and Musa acuminata catalases. They were found to differ slightly. Using known features of catalase active sites, four pre-requisite criteria were defined to find such sites: (1) Position of tyrosine axial to heme determined by X-ray diffraction, (2) 7 conserved amino acids in the active site found by sequence alignment, (3) favourable docking energy, and (4) presence of an unobstructed long tunnel that leads the ligand to the active site. Two differing potential docking sites were found for both FHIA18 and Williams that fit a maximum number of criteria. In terms of 1D sequence, the region of the docking site for Williams is within the catalase domains as seen upon NCBI blast. The counterpart of FHIA18 for the same region is not. This sequence difference between FHIA18 and Williams affects the best docking site in FHIA18 and Williams in silico.
Keywords: Catalase, conserved, clustering, active sites, pockets, tunnels, docking
Abstract: Bioinformatics tools are employed lately for in silico structure-function analysis of proteins. HIV protease inhibitors nelfinavir and tipranavir belong to the extended multi-ring systems. The intermolecular interactions made by the functional groups of the different residues on the protein molecule are probed with the help of computational tools for protein homology studies so as to identify the functional residues, create single, double, triple mutations using, different bioinformatics servers and to observe the…changes brought therein by docking. BLAST, RosettaDesign, PatchDock, Chimera were used in the present study for identifying the inhibitors as better drug targets. The HIV protease-nelfinavir complex (PDB code: 1OHR) and HIV protease V82F/I84V double mutant-tipranavir complex (PDB code: 1D4S) were used as templates for introducing mutations on the HIV protease active site. In this study a structure-based computer-assisted search for the comparison of the two inhibitors of HIV protease was carried out. The results suggest that the two inhibitors nelfinavir and tipranavir could be used for treatment of AIDS by targeting the enzyme HIV protease as neither of the two inhibitors exhibit any cross-reactivity with other human proteins, they readily bind to the mutated enzyme active site and still remain linked with the enzyme-substrate complex in the presence of water molecules. The inhibitor nelfinavir undergoes several changes in hydrogen bonds formation with the introduction of mutations on the HIV protease active site. It either has a positive or a negative inhibitory effect on HIV protease and forms new hydrogen bonds with a shorter bond lengths. Nelfinavir also seems to be an inhibitor of a more narrow specificity as it shows changes in binding bringing thereby conformational changes in the native enzyme. Tipranavir on the other hand seems to be a broad specificity inhibitor as no changes in the bond lengths with the introduction of mutations are observed. Of the two inhibitors tipranavir could be targeted more effectively for designing future drug analogues as it is less vulnerable to mutations. The HIV mutants reported herein could also be used for preliminary identification of specific inhibitors as drugs that may alter the HIV protease activity for medicinal use.
Keywords: HIV, in silico analysis, mutation, nelfinavir, protease, tipranavir
Abstract: The incidence of human infections by the fungal pathogen Candida species has been increasing in recent years. Enolase is an essential protein in fungal metabolism. Sequence data is available for human and a number of medically important fungal species. An understanding of the structural and functional features of fungal enolases may provide the structural basis for their use as a target for the development of new anti-fungal drugs. We have obtained the sequence of the…enolase of Candida krusei (C. krusei), as it is a significant medically important fungal pathogen. We have then used multiple sequence alignments with various enolase isoforms in order to identify C. krusei specific amino acid residues. The phylogenetic tree of enolases shows that the C. krusei enolase assembles on the tree with the fungal genes. Importantly, C. krusei lacks four amino acids in the active site compared to human enolase, as revealed by multiple sequence alignments. These differences in the substrate binding site may be exploited for the design of new anti-fungal drugs to selectively block this enzyme. The lack of the important amino acids in the active site also indicates that C. krusei enolase might have evolved as a member of a mechanistically diverse enolase superfamily catalying somewhat different reactions.
Abstract: Bovine viral diarrhea virus (BVDV) is a member of the Flaviviridae family of viruses and constitutes a very important pathogen for livestock around the world . The viral helicase is an enzyme essential for the proliferation and transmission of the virus. In this work a 3D-model of the BVDV helicase was produced using homology modelling techniques and the known 3D-structure of the hepatitis C helicase of the Flaviviridae family as template, in an attempt to…provide the means for structure-based design of novel anti-BVDV agents.
Abstract: Identification of novel drug targets in silico in Vibrio vulnificus is important as it is one of the emerging pathogenic microorganisms. Glutamate racemase, an important constituent of bacterial cell wall is chosen for structure prediction using homology modeling. With the aid of tools and softwares like MODELLER and Swiss-PdbViewer, the 3D structure is predicted and the final model is refined by energy minimization. The quality of the refined model is assessed using PROCHECK. The interaction between…the predicted structure of glutamate racemase and its potential inhibitors namely L-serine O-sulfate, (2R,4R)-2-amino-4-(2-benzo[b]thienyl)methyl pentanedioic acid, aziridino glutamate, exiguaquinol, γ-2 naphthylmethyl-D-glutamate and D-glutamine is analysed in silico by Autodock. The results indicate that certain residues like Asp13, Tyr45, Gly46, Asn78, Thr79, Cys185, His187 are highly conserved across the active site stretches of different bacterial species and may possibly assume precedence over the other residues for inhibitory action. This study provides an insight into the structure of glutamate racemase in V. vulnificus and also gives an idea about potential sites responsible for inhibitory action that could further be substantiated by experimental investigations.
Abstract: Living organisms often exist in uncertain environments where changes are the norm. Cellular systems therefore require resilient regulatory mechanisms for timely and stable adaptation. Among various regulation motifs, multiple feedback control emerges as a common theme. The tryptophan operon system in Escherichia coli regulates the production of intracellular tryptophan using an apparatus of three feedback mechanisms: repression, attenuation and enzyme inhibition; each provides essentially the same function but operates in distinctly different…ways. Here we aim to understand the roles of each loop by studying transient dynamics of the system to perturbations of different types; to reveal the underlying relationships between individual control mechanisms and macroscopic behaviour. We develop an S-systems approximation of an existing model for the system and characterise transient dynamics by introducing two measurable quantities: maximum disturbance (MD) and recovery time (RT). Our simulation results showed that combined regulation using all three feedback mechanisms significantly increases system stability, broadening the range of kinetic parameters for stable behaviour. Enzyme inhibition was shown to directly control the disturbance level in system variables after perturbations. Attenuation, on the other hand, was found to speed up system recovery whereas repression lengthens recovery time. The method developed in this paper and the defined transient dynamics measurements can be applied to other cellular systems.
Abstract: The effects of abscisic acid (ABA) induction on Arabidopsis thaliana transcriptome have been investigated by various expression studies. We have assembled and analyzed data from available expression studies related to ABA signaling in Arabidopsis along with other available microarray data, functional annotations and information related to occurrence of cis-regulatory elements in promoters of Arabidopsis genes in a database called TRABAS. TRABAS is expected to provide a simple, user-friendly platform to facilitate…the study of different aspects of ABA mediated transcription regulation and is freely available at http://www.bioinformatics.org/trabas/.
Keywords: ABA signaling, expression profile, cis-regulatory element, gene ontology
Abstract: Although butyrylcholinesterase (BChE) is ubiquitous in the human system, its physiological function has often been questioned. Yet BChE has been the subject of active research since its discovery six decades ago. From an evolutionary view point, its stabilized existence even in absence of physiological function spared it from extinction. Herein, we present results on the amino acid residues essential for its stability using CUPSAT server. Out of the 523 amino acids analyzed, 168 were identified to…be vital for stability of the protein, and further categorized into three classes. The first class has 82 sites wherein any amino acid substitution results in instability. The second class has 52 sites where on one amino acid substitution alone stability is observed, while the third class has 34 sites where even on two different substitutions, stability is maintained. These sites are distributed throughout the different categories of protein secondary structure, with the order of priority: random coils, α-helices and β-strands. Multiple sequence alignment of BChE showed that most of these residues (85.1%) are within the conserved region, while the few that are not at the conserved region are proposed to be unique residues (14.9%) to the protein which do not show identity with other known homologs. Moreover, majority of the amino acid residues in the functional regions of human BChE do not show instability upon point mutation, indicative of the residue-wise separation for stability and function. Specifically, the active site S198 on mutation does not show instability, while L318P is highly unstable. In addition, S53, G212 and W430 are not involved in its stability and in fact the protein is stable even with all other 19 substitutions. In conclusion, this study bodes well as a forerunner for mutation and protein engineering studies of BChE.
Abstract: SIRE1 is a 2,000-copy member of the Ty1/copia retroelement family found in the soybean genome and is closely related to sireviruses found in the genomes of other legumes. Although these elements closely resemble typical plant members of the Ty1/copia family, they are unusual in that they possess an envelope-like coding region immediately downstream of the reverse transcriptase gene. Despite its copy number, very few members of the SIRE1 family are currently present in publicly available…genomic assemblies or draft contigs. However, fragments of family members are well-represented as BAC-ends in the GenBank Genome Survey Sequence database. This database was queried using the 5' and 3' ends of SIRE1 in order to catalog sequences into which SIRE1 members have integrated. Seven hundred and eighty-one unique SIRE1 insertions were identified and the majority of insertion sites constituted other repetitive elements, including Class I and Class II transposable elements and satellite DNAs. Ninety-four insertions were in single- or low-copy number sequences and three of these were homologous to characterized protein-coding genes. Examination of the ten bases flanking either side of SIRE1 revealed no clear consensus sequence, but the the distributions of A, C, G, and T at most of the positions were biased with strong statistical significance.
Abstract: Gene expression profiles of 16 Alzheimer's (AD) patients, diagnosed as incipient or healthy using Mini-Mental State Examination and Neurofibrillary Tangles scores, were analyzed to validate the reclassification of 4 subjects previously identified as being misdiagnosed. Three datasets were created using original classifications (D1), new classifications, based on a misclassification algorithm (D2), and by removing questionable subjects (D3). Mixed model analysis was used to identify differentially expressed genes. Many genes related to the…nervous system and AD were found to be differentially expressed in D2 and D3, while few genes, none related to NS or AD, were found using D1. Several additional relevant genes were found when using D2 versus D3, which were likely due to differences in sample size. These results suggest the 4 questionable subjects were likely misclassified in D1. The similarities between results obtained using D2 and D3 provides further evidence of the adequacy of the misclassification algorithm.
Keywords: Gene expression, Alzheimer's Disease, misclassification algorithm, mixed model analysis, Mini-Mental Sate Examination (MMSE) and Neurofibrillary Tangles