bluuebunny/crossref_metadata_2025 huggingface dataset:
AMIGOS: A Method for the Inspection of Genomic Organisation or	Structure and its Application to Characterise Conserved Gene Arrangements
Authors: Merkl Rainer
Published: January 2025

In order to identify and to characterise gene clusters conserved in microbial genomes, the algorithm AMIGOS was developed. It is based on a categorisation of genes using a predefined set of gene functions (GFs). After the categorisation of all genes of a genome and based on their location on a replicon, distances between GFs were determined and stored in genome-specific matrices. These matrices were used to identify GF clusters like those strictly conserved in 13 archaeal, in 47 bacterial genomes and in the combination of the sets. Within the combined set of these 60 microbial genomes, there exist only two strictly conserved clusters harbouring two ribosomal genes each, namely those for L4, L23 and L22, L29.

In order to characterise less strictly conserved GF clusters, content of genomes i.e. matrices were analysed pairwise. Resulting clusters were merged to (meta-) clusters if their content overlapped. A scoring system named cons $_{CL}$ was developed. It quantifies conservedness of cluster membership for individual GFs.

For the genome of Escherichia coli it was shown that a grouping of cluster elements on cons $_{CL}$ values dissected the clusters into smaller sets. These sets were frequently overlapped by known transcriptional units (TUs). This finding justifies the usage of cons $_{CL}$ scores to predict TU membership of genes. In addition, cons $_{CL}$ values provide a sound basis for non-homologous gene annotation. Based on cons $_{CL}$ values, examples of conserved clusters containing annotated genes and single ones with unknown function are given.
MACO: A Gapped-Alignment Scoring Tool for Comparing Transcription	Factor Binding Sites
Authors: Su Gang , Mao Binchen , Wang Jin
Published: January 2025

We have implemented a novel gapped-alignment algorithm to compare Position Frequency Matrices (PFMs) for Transcription Factor Binding Sites. The application compares an input PFM with those collected from public databases and outputs similarity scores, sequence alignments and related PFM clusters. MACO is freely accessible on a web server located at www.nicemice.cn/bioinfo/MACO. Source code is distributed upon request to the authors.
SSToSS – Sequence-Structural Templates of Single-Member	Superfamilies
Authors: Chakrabarti Saikat , Manohari Gowri , Pugalenthi Ganesan , Sowdhamini Ramanathan
Published: January 2025

The presence of sequence homologues and the availability of structural information of proteins enable better understanding of the biological function of a protein family. A majority of entries in protein structural databank are single member superfamilies for which it is hard to derive motifs due to the paucity of structural homologues. Important conserved segments for these superfamilies have been identified and compiled into a database, SSToSS (Sequence Structural Templates of Single member Superfamily). Conserved regions, recognized by permitted amino acid exchanges, are mapped on the structure and various structural features (solvent accessibility, secondary structure content, hydrogen bonding and residue packing) are examined. These conserved segments with high structural feature content are projected as sequence-structural templates for the particular superfamily member. Interactive three-dimensional displays of the templates in three-dimensional structure (in Chime® and RASMOL) are provided for better understanding and visualization. In SSToSS database, we also provide the application of sequence-structural templates in three different areas: multiple-motif based sequence search, multiple sequence alignment and homology modeling. In each case, the inclusion of the sequence-structural templates can give rise to sensitive and accurate results. This enables the inclusion of singletons to provide added value to the recognition of additional members, comparative modeling and in designing experiments.
Analysis and Comparison of Benchmarks for Multiple Sequence	Alignment
Authors: Blackshields Gordon , Wallace Iain M. , Larkin Mark , Higgins Desmond G.
Published: January 2025

The most popular way of comparing the performance of multiple sequence alignment programs is to use empirical testing on sets of test sequences. Several such test sets now exist, each with potential strengths and weaknesses. We apply several different alignment packages to 6 benchmark datasets, and compare their relative performances. HOMSTRAD, a collection of alignments of homologous proteins, is regularly used as a benchmark for sequence alignment though it is not designed as such, and lacks annotation of reliable regions within the alignment. We introduce this annotation into HOMSTRAD using protein structural superposition. Results on each database show that method performance is dependent on the input sequences. Alignment benchmarks are regularly used in combination to measure performance across a spectrum of alignment problems. Through combining benchmarks, it is possible to detect whether a program has been over-optimised for a single dataset, or alignment problem type.
Estimation of Membrane Proteins in the Human Proteome
Authors: Ahram Mamoun , Litou Zoi I. , Fang Ruihua , Al-Tawallbeh Ghaith
Published: January 2025

Genomics and proteomics have added valuable information to our knowledgebase of the human biological system including the discovery of therapeutic targets and disease biomarkers. However, molecular profiling studies commonly result in the identification of novel proteins of unknown localization. A class of proteins of special interest is membrane proteins, in particular plasma membrane proteins. Despite their biological and medical significance, the 3-dimensional structures of less than 1% of plasma membrane proteins have been determined. In order to aid in identification of membrane proteins, a number of computational methods have been developed. These tools operate by predicting the presence of transmembrane segments. Here, we utilized five topology prediction methods (TMHMM, SOSUI, waveTM, HMMTOP, and TopPred II) in order to estimate the ratio of integral membrane proteins in the human proteome. These methods employ different algorithms and include a newly-developed method (waveTM) that has yet to be tested on a large proteome database. Since these tools are prone for error mainly as a result of falsely predicting signal peptides as transmembrane segments, we have utilized an additional method, SignalP. Based on our analyses, the ratio of human proteins with transmembrane segments is estimated to fall between 15% and 39% with a consensus of 13%. Agreement among the programs is reduced further when both a positive identification of a membrane protein and the number of transmembrane segments per protein are considered. Such a broad range of prediction depends on the selectivity of the individual method in predicting integral membrane proteins. These methods can play a critical role in determining protein structure and, hence, identifying suitable drug targets in humans.
MemO: A Consensus Approach to the Annotation of a Protein's	Membrane Organization
Authors: Davis Melissa J. , Zhang Fasheng , Yuan Zheng , Teasdale Rohan D.
Published: January 2025

Membrane organization describes the relationship of proteins to the membrane, that is, whether the protein crosses the membrane or is integral to the membrane and its orientation with respect to the membrane. Membrane organization is determined primarily by the presence of two features which target proteins to the secretory pathway: the endoplasmic reticulum signal peptide and the α-helical transmembrane domain. In order to generate membrane organization annotation of high quality, confidence and throughput, the Membrane Organization (MemO) pipeline was developed, incorporating consensus feature prediction modules with integration and annotation rules derived from biological observations. The pipeline classifies proteins into six categories based on the presence or absence of predicted features: Soluble, intracellular proteins; Soluble, secreted proteins; Type I membrane proteins; Type II membrane proteins; Multi-span membrane proteins and Glycosylphosphatidylinositol anchored membrane proteins. The MemO pipeline represents an integrated strategy for the application of state-of-the-art bioinformatics tools to the annotation of protein membrane organization, a property which adds biological context to the large quantities of protein sequence information available.
In Silico Modeling and Hydrogen Peroxide	Binding Study of Rice Catalase
Authors: Sekhar Pagadala Nataraj , Kishor Polavarapu B. Kavi , Reddy Lakkireddy Ananda , Mondal Prosenjit , Dash Ardhendu K. , Kar Manoranjan , Mohanty Satya , Sabat Surendra C.
Published: January 2025

Homology modeling of the catalase, CatC cloned and sequenced from rice (Oryza sativa L., cv Ratna an Indica cultivar) has been performed based on the crystal structure of the catalase CatF (PDB code 1m7s) by using the software MODELLER. With the aid of molecular mechanics and molecular dynamics methods, the final model is obtained and is further assessed by PROCHECK and VERIFY – 3D graph, which show that the final refined model is reliable. With this model, a flexible docking study with the hydrogen peroxide, the substrate for catalase, is performed and the results indicate that Arg310, Asp343 and Arg346 in catalase are three important determinant residues in binding as they have strong hydrogen bonding contacts with the substrate. These hydrogen-bonding interactions play an important role for the stability of the complex. Our results may be helpful for further experimental investigations.
Automated Molecular Library Generation of Proteic Fragments by	Virtual Proteolysis for Molecular Modelling Studies
Authors: Librando Vito , Gullotto Danilo , Minniti Zelica
Published: January 2025

This paper presents a computer aided design method useful for simulation of a set of proteolytic cleavages upon target proteins obtained from the Brookhaven Data Bank. The method was developed by using algorithms that are able to interface themselves with other software environments, in order to assist computer analyses in the molecular modelling field, and allowing the generation of molecular libraries containing protein fragments produced by simulated proteolysis. These libraries include structures that differ for several amino acid deletions upon specified regions of the primary sequence. Target residues chosen for the simulation are compatible with enzymatic proteolysis methods used in conventional laboratory procedures. Furthermore, algorithms were able to identify a set of chemical-physical properties of the starting proteins, leading the simulation to find out the most suitable residues for proteolysis. The goal of these strategies is to generate fragments that are leaded to maintain the native-like condition of starting molecules, avoiding loss of conformational characteristics of the original tertiary structure. Proteins chosen for generating proteolytic libraries were represented by naphthalene 1,2 dioxygenase and Rigidoporus lignosus laccase.
Sequence Analysis of the Receptor Activity-Modifying Proteins	Family, New Putative Peptides and Structural Conformation Inferenc
Authors: Benítez-Páez Alfonso
Published: January 2025

The Receptor Activity-Modifying Proteins (RAMP) is a family constituted by a single N-terminal extracellular domain and a transmembrane region ending in a short cytoplasmic region. Due to their specific role in modulating the specificity of ligand binding in many class II G-Protein Coupled Receptors, these proteins are awaiting further characterization and elucidation of their structure. This was the aim of this study. We were able to find 13 new RAMP sequences including new protein sequences and predicted peptides from Expressed Sequence Tags and genomic DNA, all of them annotated in databases such as GeneBank, EMBL, Swissprot and ENSEMBL. The predicted peptides came from an array of different organisms including Teleostei and Elasmobranchii species, of which the latter was the most ancient RAMP sequence found. It was also possible to efficiently predict the 1D structure of the extracellular RAMP domain and its 3D conformation was inferred through a combination of bioinformatic approaches such as threading. The 1D structure of the extracellular RAMP domain was predicted as three α-helix domain. The most highly conserved residues in the RAMP family were found to be involved in critical functions. Bioinformatic data mining and multiple sequence alignment analysis were crucial for improving the characterization of RAMP proteins and prediction of their 1D and 3D configurations.
Primer Design for Whole Genome Amplification Using Genetic	Algorithms
Authors: Png Adrian E.H. , Choo Keng Wah , Lee Cheryl I.P. , Leong Siew Hong , Kon Oi Lian
Published: January 2025

Whole Genome Amplification (WGA) is an important process to increase limiting amounts of genomic DNA prior to genomic analyses. Current amplification methods based on primer extension or strand displacement principles employ primers of partially or totally random sequence. In this paper, we present a method using Genetic Algorithms to optimize a single primer design to be used in a primer extension reaction to achieve unbiased WGA. Computational simulation and prediction of a suitable primer proposed two candidates NYP6-1 (ATCTCA) and NYP6-2 (TGAGAT). NYP6-1 amplified to a maximum length of 2537 base pairs (bp), had genome coverage of approximately 45.62%, with an average of 493 and variance of 163 amplicons per 1 megabasepairs (Mb). NYP6-2 amplified to a maximum length of 2926 bp and covered 54.35% of the genome with an average of 579 and a variance of 191 amplicons per Mb. In contrast, the original primer used in Degenerate Oligonucleotide-Primed PCR (DOP-PCR) had coverage of 20.93%, an average of 74 and variance of 188 amplicons per Mb when extended up to a length of 2000 bp. Successful WGA of miniscule amounts of genomic DNA requires the amplification method used to resolve issues on efficiency, accurate representation of the whole genome and ability to degraded DNA. The sequence NYP6-2 discovered using our method can be confidently used in a primer extension based protocol to perform quantitatively unbiased WGA.
Improving the Performance of an SVM-Based Method for Predicting	Protein-Protein Interactions
Authors: Dohkan Shinsuke , Koike Asako , Takagi Toshihisa
Published: January 2025

Predicting the interactions between all the possible pairs of proteins in a given organism (making a protein-protein interaction map) is a crucial subject in bioinformatics. Most of the previous methods based on supervised machine learning use datasets containing approximately the same number of interacting pairs of proteins (positives) and non-interacting pairs of proteins (negatives) for training a classifier and are estimated to yield a large number of false positives. Thinking that the negatives used in previous studies cannot adequately represent all the negatives that need to be taken into account, we have developed a method based on multiple Support Vector Machines (SVMs) that uses more negatives than positives for predicting interactions between pairs of yeast proteins and pairs of human proteins. We show that the performance of a single SVM improved as we increased the number of negatives used for training and that, if more than one CPU is available, an approach using multiple SVMs is useful not only for improving the performance of classifiers but also for reducing the time required for training them. Our approach can also be applied to assessing the reliability of high-throughput interactions.
Detailed Comparison of the Protein-Ligand Docking Efficiencies of	GOLD, a Commercial Package and ArgusLab, a Licensable Freeware
Authors: Joy Saju , Nair Parvathy S. , Hariharan Ramkumar , Pillai M. Radhakrishna
Published: January 2025

Molecular docking and virtual screening based on molecular docking have become an integral part of many modern structure-based drug discovery efforts. Hence, it becomes a useful endeavor to evaluate existing docking programs, which can assist in the choice of the most suitable docking algorithm for any particular study. The objective of the current study was to evaluate the ability of ArgusLab 4.0, a relatively new molecular modeling package in which molecular docking is implemented, to reproduce crystallographic binding orientations and to compare its accuracy with that of a well established commercial package, GOLD. The study also aimed to evaluate the effect of the nature of the binding site and ligand properties on docking accuracy. The three dimensional structures of a carefully chosen set of 75 pharmaceutically relevant protein-ligand complexes were used for the comparative study. The study revealed that the commercial package outperforms the freely available docking engine in almost all the parameters tested. However, the study also revealed that although lagging behind in accuracy, results from ArgusLab are biologically meaningful. This taken together with the fact that ArgusLab has an easy to use graphical user interface, means that it can be employed as an effective teaching tool to demonstrate molecular docking to beginners in this area.
A Database of Simple Sequence Repeats from Cereal and Legume	Expressed Sequence Tags Mined in silico: Survey and Evaluation
Authors: Jayashree B. , Punna Ramu , Prasad P. , Bantte Kassahun , Hash C. Tom , Chandra Subhash , Hoisington David A. , Varshney Rajeev K.
Published: January 2025

Simple sequence repeats (SSRs) or microsatellites are an important class of molecular markers for genome analysis and plant breeding applications. In this paper, the SSR distributions within ESTs from the legumes soybean (Glycine max, representing 135.86 Mb), medicago (Medicago truncatula, 121.1 Mb) and lotus (Lotus japonicus, 45.4 Mb) have been studied relative to the distributions in cereals such as sorghum (Sorghum bicolor, 98.9 Mb), rice (Oryza sativa, 143.9 Mb) and maize (Zea mays, 183.7 Mb). The relative abundance, density, composition and putative annotations of di-, tri-, tetra- and penta-nucleotide repeats have been compared and SSR containing ESTs (SSR-ESTs) have been clustered to give a non-redundant set of EST-SSRs, available in a database. Further, a subset of such candidate EST-SSRs from sorghum have been tested for their ability to detect polymorphism between Striga-susceptible, stay-green drought tolerant mapping population parent 'E 36-1' and its Striga-resistant, non-stay-green counterpart 'N13'. Primer sets for 64% of the EST-SSRs tested produced a clear and specific PCR product band and 34% of these detected scorable polymorphism between the N13 and E 36-1 parental lines. Over half of these markers have been genotyped on 94 RILs from the (N13 × E 36-1)-based mapping population, with 42 markers mapping onto the ten sorghum linkage groups. This establishes the value of this database as a resource of molecular markers for practical applications in cereal and legume genetics and breeding. The primer pairs for non-redundant EST-SSRs have been designed and are freely available through the database (http://intranet.icrisat.org/gt1/ssr/ssrdatabase.html).
Prediction of 3-Dimensional Structure of Salivary Odorant-Binding	Protein-2 of the Mosquito Culex Quinquefasciatus, the	Vector of Human Lymphatic Filariasis
Authors: Paramasivan Rajaiah , Sivaperumal Ramamoorthy , Dhananjeyan Kutty Jegadeeswaran , Thenmozhi Velayutham , Tyagi Brij Kishore
Published: January 2025

Olfaction of insects is currently recognized as the major area of research for developing novel control strategies to prevent mosquito-borne infections. A 3-dimensional model (3D) was developed for the salivary gland odorant-binding protein-2 of the mosquito Culex quinquefasciatus, a major vector of human lymphatic filariasis. A homology modeling method was used for the prediction of the structure. For the modeling, two template proteins were obtained by mGenTHERADER, namely the high-resolution X-ray crystallography structure of a pheromone-binding protein (ASP1) of Apis mellifera L., [1R5R:A] and the aristolochene synthase from Penicillium roqueforti [1DI1:B]. By comparing the template protein a rough model was constructed for the target protein using MODELLER, a program for comparative modelling. The structure of OBP of the mosquito Culex quinquefasciatus resembles the structure of pheromone-binding protein ASP1 of Apis mellifera L., [1R5R:A]. From Ramachandran plot analysis it was found that the portion of residues falling into the most favoured regions was 86.0%. The predicted 3-D model may be further used in characterizing the protein in wet laboratory.
MOVE: A Multi-Level Ontology-Based Visualization and Exploration	Framework for Genomic Networks
Authors: Bosman Diederik W.J. , Blom Evert-Jan , Ogao Patrick J. , Kuipers Oscar P. , Roerdink Jos B.T.M.
Published: January 2025

Among the various research areas that comprise bioinformatics, systems biology is gaining increasing attention. An important goal of systems biology is the unraveling of dynamic interactions between components of living cells (e.g., proteins, genes). These interactions exist among others on genomic, transcriptomic, proteomic and metabolomic levels. The levels themselves are heavily interconnected, resulting in complex networks of different interacting biological entities. Currently, various bioinformatics tools exist which are able to perform a particular analysis on a particular type of network. Unfortunately, each tool has its own disadvantages hampering it to be used consistently for different types of networks or analytical methods. This paper describes the conceptual development of an open source extensible software framework that supports visualization and exploration of highly complex genomic networks, like metabolic or gene regulatory networks. The focus is on the conceptual foundations, starting from requirements, a description of the state of the art of network visualization systems, and an analysis of their shortcomings. We describe the implementation of some initial modules of the framework and apply them to a biological test case in bacterial regulation, which shows the relevance and feasibility of the proposed approach.
Evolved Cellular Automata for Protein Secondary Structure	Prediction Imitate the Determinants for Folding Observed in Nature
Authors: Chopra Paras , Bender Andreas
Published: January 2025

We demonstrate the first application of cellular automata to the secondary structure predictions of proteins. Cellular automata use localized interactions to simulate global phenomena, which resembles the protein folding problem where individual residues interact locally to define the global protein conformation. The protein's amino acid sequence was input into the cellular automaton and rules for updating states were evolved using a genetic algorithm. An optimized accuracy (Q3) for the RS126 and CB513 dataset of 58.21% and 56.51%, respectively, could be obtained. Thus, the current work demonstrates the applicability of a rather simple algorithm on a problem as complex as protein secondary structure prediction.
GUIMACS – A Java Based Front End for GROMACS
Authors: Kota Pradeep
Published: January 2025

Molecular dynamics simulations have gained importance due to their ability to provide valuable insights into understanding structure-function relationships of biological macromolecules. With increasing computational speeds there has been a substantial demand for optimization of simulation algorithms to obtain results even faster. With this on one hand, the need for ease of operation lies on the other. GUI front end programs are important appurtenances to ease the use of command line programs. Effective use of command line based programs requires basic knowledge of the UNIX shell and at least one of the UNIX based text editors, making it difficult for pure biologists to use them efficiently. GROMACS, a widely used suite of molecular dynamics simulation and analysis programs, is no exception to this. As a matter of fact, the increasing dependency of experimental procedures on computational methods for accentuating certain key experimental findings increases the need for interactivity in use of command-line based packages.

GUIMACS is a Java based user-interactive front-end interface for the Linux version of GROMACS (version 3.3). GUIMACS runs as a standalone application with Multiple Document Interface (MDI) enabling its users to run and/or analyze multiple molecular dynamics simulations simultaneously.
In Silico Identification and Characterization	of a Putative Phosphatidylinositol 4-Phosphate 5-Kinase (PIP5K) Gene in	Eimeria Tenella
Authors: Ling King-Hwa , Loo Shu-San , Rosli Rozita , Shamsudin Mariana Nor , Mohamed Rahmah , Wan Kiew-Lian
Published: January 2025

Phosphatidylinositol 4-phosphate 5-kinases (PIP5Ks) play diverse roles in the cellular biology of many organisms, including signal transduction, secretion and vesicular trafficking, and regulation of cytoskeleton assembly. Discovery of the PIP5K gene in Eimeria tenella may shed light on its role in the biology of this avian protozoan, and afford further understanding of the cell-host interaction, particularly during the invasion process. In this study, we report the identification of the PIP5K coding region in the genome sequence of Eimeria tenella using in silico gene prediction approaches. Prediction of the PIP5K coding sequence was confirmed by mapping the full-length cDNA sequence, generated via the Rapid Amplification of cDNA Ends (RACE) method, to the genomic sequence. The putative PIP5K gene of Eimeria tenella is located on the complementary strand of the E1080B12.b1 contig, and comprises 12 exons. Further analysis showed that the coding region spans from exon 1 to exon 7, with all exons obeying the adopted 'gt ... ag' splicing rule of intronic sequences. Consensus of the hexameric 5' donor-splice site was deduced as GTRDBB ... and the consensus for the 3' acceptor-splice sites as ...BHDYAG. The gene encodes a 252-amino acid residue protein. Domain search and protein fold recognition analyses provide compelling evidences that the deduced protein is a PIP5K.
Frameshift Signals in Genes Associated with the Circular	Code
Authors: Ahmed Ahmed , Frey Gabriel , Michel Christian J.
Published: January 2025

Three sets of 20 trinucleotides are preferentially associated with the reading frames and their 2 shifted frames of both eukaryotic and prokaryotic genes. These 3 sets are circular codes. They allow retrieval of any frame in genes (containing these circular code words), locally anywhere in the 3 frames and in particular without start codons in the reading frame, and automatically with the reading of a few nucleotides. The circular code in the reading frame, noted X, which can deduce the 2 other circular codes in the shifted frames by permutation, is the information used for analysing frameshift genes, i.e. genes with a change of reading frame during translation. This work studies the circular code signal around their frameshift sites. Two scoring methods are developed, a function P based on this code X and a function Q based both on this code X and the 4 trinucleotides with identical nucleotides. They detect a significant correlation between the code X and the −1 frameshift signals in both eukaryotic and prokaryotic genes, and the +1 frameshift signals in eukaryotic genes.
In Silico Detection of Binding Mode of	J-Superfamily Conotoxin pl14a with Kv1.6 Channel
Authors: Mondal Sukanta , Babu Rajasekaran Mohan , Bhavna Rajasekaran , Ramakumar Suryanarayanarao
Published: January 2025

A novel conotoxin pl14a containing 25 amino acid residues with an amidated C-terminus from vermivorous cone snail, Conus planorbis belongs to J-conotoxin superfamily and this is the first conotoxin, which inhibits both nicotinic acetylcholine receptor subtypes and Kv1.6 channel. We have attempted through bioinformatics approaches to elucidate the extent of specificity of pl14a towards Kv1 channel subtypes (Kv1.1-Kv1.6). Our work provides rationale for the relatively high specificity and binding mode of pl14a to Kv1.6 channel.The pl14a peptide contains two types of structural elements, namely the putative dyad (Lys18 and Tyr19) and basic residue ring constituted of arginine residues. We have carried out in silico docking studies so as to assess the contribution of one or combination of both structural elements of pl14a in blocking of Kv1.6 channel. For this purpose, we have built by homology modelling, the theoretical 3D structure of Kv1.6 channel based on the available crystal structure of mammalian shaker Kv1.2 channel. Docking studies suggest that positively charged residues ring may be involved in the blocking mechanism of Kv1.6 channel. The models suggest that the peptide interacts with negatively charged extracellular loops and pore-mouth of the potassium channel and blocks the channel by covering the pore as a lid, akin to previously proposed blocking mechanism of κM-conotoxin RIIIK from Conus radiatus to Tsha1 potassium channel. The newly detected pharmacophore for pl14a interacting with Kv1.6 channel provides a pointer to experimental work to validate the observations made here. Based on differences in the number and distribution of the positively-charged residues in other conopeptides from the J-superfamily, we hypothesize different selectivity profiles against subtypes of the potassium channels for these conopeptides.
ISN1 Nucleotidases and HAD Superfamily Protein Fold: In	silico Sequence and Structure Analysis
Authors: Srinivasan Bharath , Balaram Hemalatha
Published: January 2025

cN-II class of 5' purine nucleotidases exhibit specificity for IMP/GMP and belong to the HAD (haloacid dehalogenase) superfamily of hydrolases. The recently identified ISN1 class of IMP specific 5'-nucleotidases occurring in yeast, fungi and certain Plasmodia lack sequence homology with the cN-II class of enzymes. We show from analysis of motif and fold conservation that ISN1s also belong to the HAD superfamily. This identification adds a new novel member to this superfamily.
nWayComp: A Genome-Wide Sequence Comparison Tool for Multiple	Strains/Species of Phylogenetically Related Microorganisms
Authors: Yao Jiqiang , Lin Hong , Doddapaneni Harshavardhan , Civerolo Edwin L.
Published: January 2025

The increasing number of whole genomic sequences of microorganisms has led to the complexity of genome-wide annotation and gene sequence comparison among multiple microorganisms. To address this problem, we have developed nWayComp software that compares DNA and protein sequences of phylogenetically-related microorganisms. This package integrates a series of bioinformatics tools such as BLAST, ClustalW, ALIGN, PHYLIP and PRIMER3 for sequence comparison. It searches for homologous sequences among multiple organisms and identifies genes that are unique to a particular organism. The homologous gene sets are then ranked in the descending order of the sequence similarity. For each set of homologous sequences, a table of sequence identity among homologous genes along with sequence variations such as SNPs and INDELS is developed, and a phylogenetic tree is constructed. In addition, a common set of primers that can amplify all the homologous sequences are generated. The nWayComp package provides users with a quick and convenient tool to compare genomic sequences among multiple organisms at the whole-genome level.
Microsatellite Motifs with Moderate GC Content Are Clustered	Around Genes on Arabidopsis thaliana Chromosome 2
Authors: Grover Atul , Sharma Prakash C.
Published: January 2025

Microsatellites, arrays of 1–6 bp sequences, are abundant in almost all the eukaryotic genomes. Their distribution in the genome is widely accepted to be differential and non random along the axis of the chromosomes. Arabidopsis thaliana genome is dominated by mononucleotide repeats, (A) $_{n}$ being the most abundant motif. In total, 39 microsatellite motifs extended to more than 100 bp in length. Of these, 8 loci are devoid of any gene in their proximity. (AG) $_{n}$ is the most abundant motif among longer repeats. The non-random distribution of microsatellite in the genome is reflected as occurrence of microsatellite clusters in the genome. In total, 3400 microsatellite clusters have been identified in the Arabidopsis genome. Chromosome 2, which is 19.7 Mb long, harbors 550 clusters accommodating 29% of all the microsatellites present on this chromosome. Further, 409 of the 6239 genes on chromosome 2 are associated with 323 microsatellite clusters. Motifs like (AGG) $_{n}$ and (ACT) $_{n}$ , show preferential accommodation in clusters that overlap with genes. Among all the microsatellite clusters that show an overlap with genes, 80% of the clusters show an overlap in such a way that the cluster ends beyond the 3'-end of the gene or starts before the 5'-end of a gene. Genes with diverse functions show association with the clusters. However, not all members of a gene family show similar associations.
Analysis of Secondary Structure Predictions of Dengue Virus Type 2	NS2B/NS3 Against Crystal Structure to Evaluate the Predictive Power of the	In Silico Methods
Authors: Othman Rozana , Wahab Habibah Abdul , Yusof Rohana , Rahman Noorsaadah Abd
Published: January 2025

Multiple sequence alignment was performed against eight proteases from the Flaviviridae family using ClustalW to illustrate conserved domains. Two sets of prediction approaches were applied and the results compared. Firstly, secondary structure prediction was performed using available structure prediction servers. The second approach made use of the information on the secondary structures extracted from structure prediction servers, threading techniques and DSSP database of some of the templates used in the threading techniques. Consensus on the one-dimensional secondary structure of Den2 protease was obtained from each approach and evaluated against data from the recently crystallised Den2 NS2B/NS3 obtained from the Protein Data Bank (PDB). Results indicated the second approach to show higher accuracy compared to the use of prediction servers only. Thus, it is plausible that this approach is applicable to the initial stage of structural studies of proteins with low amino acid sequence homology against other available proteins in the PDB.
Correlation Between the Structural Stability and Aggregation	Propensity of Proteins
Authors: Idicula-Thomas Susan , Balaji Petety V.
Published: January 2025

Protein aggregation, being an outcome of improper protein folding, is largely dependent on the folding kinetics of a protein. Previous studies have reported a positive correlation between the stability of the secondary structural elements of a protein and their rate of folding/unfolding. In this in silico study, the secondary and tertiary structures of proteins a) that form inclusion bodies on overexpression in Escherichia coli, b) that form amyloid fibrils and c) that are soluble on overexpression in E. coli are analyzed for certain features that are known to be associated with structural stability. The study revealed that the soluble proteins seem to have a higher rate of folding (based on contact order) and a lower percentage of exposed hydrophobic residues as compared to the inclusion body forming or amyloidogenic proteins. The soluble proteins also seem to have a more favored helix and strand composition (based on the known secondary structural propensities of amino acids). The secondary structure analyses also reveal that the evolutionary pressure is directed against protein aggregation. This understanding of the positive correlation between structural stability and solubility, along with the other parameters known to influence aggregation, could be exploited in the design of mutations aimed at reducing the aggregation propensity of the proteins.
An in silico Analysis of Cytochrome c from	Phanerochaete chrysosporium: Its Amino Acid Sequence and	Characterization of Gene Structural Elements
Authors: Bumpus John A. , Trax Mark , Reisdorph Ashley , Boyd Cindi , Gilbert Damien , Techau Sara , Ventullo Roy M.
Published: January 2025

An in silico approach was used to investigate cytochrome c and the cytochrome c gene of Phanerochaete chrysosporium. The cytochrome c gene contains four introns. Omission of the introns reveals a DNA sequence coding for a complete predicted amino acid sequence for P. chrysosporium cytochrome c consistent with those of other cytochromes c. Fungal cytochromes c often have a short N-terminal peptide preceding a Gly that is the N-terminal amino acid in many cytochromes c. Thus a microexon codes for an N-terminal pentapeptide (MetProTyrAlaPro) in P. chrysosporium that is identical to the N-terminal pentapeptide of Schizosaccharomyces pombe, a well studied yeast, the genome of which bears more similarity to higher eukaryotes than to other fungi. The fourth intron, when omitted, reveals the presence of another microexon resulting in a sequence for the C-terminal portion of the protein and the stop codon. Interestingly, two interpretations for the sequence of this intron leads to predictions that the C-terminal sequence ends with either AlaValAsn or AlaTyr. Selected aspects of the molecular architecture of cytochrome c and regulatory control elements of the P. chrysosporium cytochrome c gene were analyzed and compared to those present in other fungi and to those present in genes for lignin peroxidases and cytochromes P-450, two important families of hemeproteins produced by this fungus.
The GTP Binding Sites Interacted with RNA-Dependent RNA Polymerase	of Classical Swine Fever Virus in de novo Initiation
Authors: Xu Zhuofei , Chao Yanjie , Si Youhui , Wang Jian , Jin Meilin , Guo Aizhen , Qian Ping , Zhou Rui , Chen Huanchun
Published: January 2025

The NS5B protein of classical swine fever virus (CSFV) is an important enzyme bearing a unique RNA-dependent RNA polymerase (RdRp) activity. The RdRp plays a crucial role in the viral replication cycle and in forming a replicase complex. However, the initiating synthesis mechanism of the CSFV RNA polymerase is unclearly described at present. Our aim is to reveal the RdRp-GTP docking sites and the effective modules of GTP initially bound to the polymerase in starting initiation of replication according to a well predicted CSFV RdRp model. Based on some known crystal structures of RNA polymerase, computational methods were used to establish the model of a CSFV RdRp. An analogous mechanism of CSFV RNA polymerase in de novo initiation was subsequently represented through docking a GTP into the structure model. The unique GTP binding pocket of the polymerase was pointed out: five residues E227, S408, R427, K435, and R439 involved in steady hydrogen bonds and two residues C407 and L232 involved in hydrophobic contact with the GTP. From a genetic evolutionary point of view, three residues C407, S408 and R427 have been suggested to be of particular importance by analysis of residue conservation. It is suggested that these crucial residues should have very significant function in the de novo initiation of the rigorous CSFV polymerase model, which can lead us to design experiments for studying the mechanism of viral replication and develop valid anti-viral drugs.
Distinct Patterns in the Regulation and Evolution of Human Cancer	Genes
Authors: Furney Simon J. , Madden Stephen F. , Kisiel Tomasz A. , Higgins Desmond G. , Lopez-Bigas Nuria
Published: January 2025

Understanding the mechanism of regulation of cancer genes and the constraints on their coding sequences is of fundamental importance in understanding the process of tumour development. Here we test the hypothesis that tumour suppressor genes and proto-oncogenes, due to their involvement in tumourigenesis, have distinct patterns of regulation and coding selective constraints compared to non-cancer genes.

Indeed, we found significantly greater conservation in the promoter regions of proto-oncogenes, suggesting that these genes are more tightly regulated, i.e. they are more likely to contain a higher density of cis-regulatory elements. Furthermore, proto-oncogenes appear to be preferentially targeted by microRNAs and have longer 3' UTRs. In addition, proto-oncogene evolution appears to be highly constrained, compared to tumour suppressor genes and non-cancer genes. A number of these trends are confirmed in breast and colon cancer gene sets recently identified by mutational screening.
NetAtlas: A Cytoscape Plugin to Examine Signaling Networks Based	on Tissue Gene Expression
Authors: Yang Longlong , Walker John R. , Hogenesch John B. , Thomas Russell S.
Published: January 2025

Graphical methods are useful for visualizing signaling networks derived from the synthesis of large bodies of literature information or large-scale experimental measurements. Software tools to filter and organize these networks allow the exploration of their inherent biological and structural properties. We have developed NetAtlas, an open-source, Java-based Cytoscape plugin for examining signaling networks in the context of tissue gene expression patterns. The tissue gene expression data available through NetAtlas consists of 79 human tissues, 61 mouse tissues, and 44 combined tissues from 3 rat strains. Users may also import their own tissue gene expression data. The NetAtlas plugin allows the creation of tissue-defined signaling networks by identifying which components are expressed in particular tissues, which components show tissue-specific expression, and which components within the network are coordinately expressed across tissues. The NetAtlas plugin is available at http://sourceforge.net/projects/netatlas/.
M@IA: A Modular Open-Source Application for Microarray Workflow	and Integrative Datamining
Authors: Le Béchec Antony , Zindy Pierre , Sierocinski Thomas , Petritis Dimitri , Bihouée Audrey , Le Meur Nolwenn , Léger Jean , Théret Nathalie
Published: January 2025

Microarray technology is a widely used approach to gene expression analysis. Many tools for microarray management and data analysis have been developed, and recently new methods have been proposed for deciphering biological pathways by integrating microarray data with other data sources. However, to improve microarray analysis and provide meaningful gene interaction networks, integrated software solutions are still needed. Therefore, we developed M@IA, an environment for DNA microarray data analysis allowing gene network reconstruction. M@IA is a microarray integrated application which includes all of the steps of a microarray study, from MIAME-compliant raw data storage and processing gene expression analysis. Furthermore, M@IA allows automatic gene annotation based on ontology, metabolic/signalling pathways, protein interaction, miRNA and transcriptional factor associations, as well as integrative analysis of gene interaction networks. Statistical and graphical methods facilitate analysis, yielding new hypotheses on gene expression data. To illustrate our approach, we applied M@IA modules to microarray data taken from an experiment on liver tissue. We integrated differentially expressed genes with additional biological information, thus identifying new molecular interaction networks that are associated with fibrogenesis.

M@IA is a new application for microarray management and data analysis, offering functional insights into microarray data by the combination of gene expression data and biological knowledge annotation based on interactive graphs. M@IA is an interactive multi-user interface based on a flexible modular architecture and it is freely available for academic users at http://maia.genouest.org.
Bioinformatics Databases and Tools in Virology Research: An	Overview
Authors: Yan Qing
Published: January 2025

Viruses are major factors of human infectious diseases. Understanding of the structure-function correlation in viruses is important for the identification of potential anti-viral inhibitors and vaccine targets. In virology research, virus-related databases and bioinformatic analysis tools are essential for discerning relationships within complex datasets about viruses and host-virus interactions. Bioinformatic analyses on viruses include the identification of open reading frames, gene prediction, homology searching, sequence alignment, and motif and epitope recognition. The predictions of features such as transmembrane domains, glycosylation sites, and protein secondary and tertiary structure are important for analyzing the structure-function relationship of proteins encoded in viral genomes. Biochemical pathway analysis can help elucidate information at the biological systems level. Microarray analysis provides methods for high throughput screening and gene expression profiling. Virus-related bioinformatics databases include those concerned with viral sequences, taxonomy, homologous protein families, structures, or dedicated to specific viruses such as influenza and herpes simplex virus (HSV). This review provides a guide and overview of computational programs for these analyses as a resource for genomics and proteomics studies in virology research. These resources are useful for understanding viral diseases, as well as for the design and development of anti-viral agents.
In silicoAnalysis of Microsatellites in	Organellar Genomes of Major Cereals for Understanding Their Phylogenetic	Relationships
Authors: Rajendrakumar Passoupathy , Biswal Akshaya Kumar , Balachandran Sena M. , Sundaram Raman M.
Published: January 2025

Microsatellites are abundant across prokaryotic and eukaryotic genomes. However, comparative analysis of microsatellites in the organellar genomes of plants and their utility in understanding phylogeny has not been reported. The purpose of this study was to understand the organization of microsatellites in the coding and non-coding regions of organellar genomes of major cereals viz., rice, wheat, maize and sorghum. About 5.8–14.3% of mitochondrial and 30.5–43.2% of chloroplast microsatellites were observed in the coding regions. About 83.8–86.8% of known mitochondrial genes had at least one microsatellite while this value ranged from 78.6–82.9% among the chloroplast genomes. Dinucleotide repeats were the most abundant in the coding and non-coding regions of the mitochondrial genome while mononucleotides were predominant in chloroplast genomes. Maize harbored more repeats in the mitochondrial genome, which could be due to the larger size of genome. A phylogenetic analysis based on mitochondrial and chloroplast genomic microsatellites revealed that rice and sorghum were closer to each other, while wheat was the farthest and this corroborated with the earlier reported phylogenies based on nuclear genome co-linearity and chloroplast gene-based analysis.