A5061962424- Computational Drug Discovery Methods
- Protein Structure and Dynamics
- Machine Learning in Bioinformatics
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Cell death mechanisms and regulation
- Genomics and Chromatin Dynamics
- Prostate Cancer Treatment and Research
- T-cell and B-cell Immunology
- Monoclonal and Polyclonal Antibodies Research
- Cancer therapeutics and mechanisms
- Prostate Cancer Diagnosis and Treatment
- Immunotherapy and Immune Responses
- Cancer, Lipids, and Metabolism
- Biochemical and Molecular Research
- Cardiomyopathy and Myosin Studies
- RNA modifications and cancer
- Glycosylation and Glycoproteins Research
- Genetics, Aging, and Longevity in Model Organisms
- Synthesis and Characterization of Heterocyclic Compounds
- Genomic variations and chromosomal abnormalities
- Chemical Synthesis and Analysis
- Metal complexes synthesis and properties
- HIV/AIDS drug development and treatment
- Cancer Genomics and Diagnostics
University of Turku
2016-2023
Turku Centre for Computer Science
2021
Åbo Akademi University
2021
Turku Centre for Biotechnology
2016-2018
Center for Systems Biology Dresden
2013-2014
TU Dresden
2013
National Centre for Biological Sciences
2009-2012
Tata Institute of Fundamental Research
2012
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug development process. In this review, we give a broad overview of current application possibilities MD discovery and pharmaceutical development. Starting from target validation step process, several examples how studies can important insights into function identified targets such as sirtuins, RAS proteins, or intrinsically disordered proteins. The role antibody design is also reviewed. lead optimization...
Chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq) has great potential for elucidating transcriptional networks, by measuring genome-wide binding of transcription factors (TFs) at high resolution. Despite the precision these experiments, identification genes directly regulated a TF (target genes) is not trivial. Numerous target gene scoring methods have been used in past. However, their suitability task and performance remain unclear, because thorough comparative...
Detection of copy number variations (CNVs) from high-throughput next-generation whole-genome sequencing (WGS) data has become a widely used research method during the recent years. However, only little is known about applicability developed algorithms to ultra-low-coverage (0.0005-0.8×) that in various and clinical applications, such as digital karyotyping single-cell CNV detection.
Myeloid cell leukemia 1 (Mcl1) is an antiapoptotic protein that plays central role in apoptosis regulation. Also, Mcl1 has the potency to resist apoptotic cues resulting up-regulation and cancer protection. A molecular probe potential specifically target thereby provoke its down-regulatory activity very essential. The aim of current study internal conformational dynamics motions binding mechanism response a series picomolar range inhibitors using explicit-solvent (MD) simulations....
G-protein coupled receptors (GPCRs) are one of the largest groups membrane proteins and popular drug targets. The work reported here attempts to perform cross-genome phylogeny on GPCRs from two widely different taxa, human versus C. elegans genomes address issues evolutionary plasticity, identify functionally related genes, orthologous relationship, ligand binding properties through effective bioinformatic approaches. Through RPS blast around 1106 nematode were given chance associate with...
Parthiban Marimuthuab** & Kalaimathy Singaraveluca Structural Bioinformatics Laboratory (SBL), Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, Turku, FI, 20520, Finlandb Department Biology, Albany State 504 College Drive, Albany, GA, USAc Information Technology, University Finland
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) is a promising antimicrobial target involved in the folate biosynthesis pathway. Although, results from crystallographic studies of HPPK have attracted great interest design novel inhibitors, mechanism action due to inhibitor binding remains questionable. Recently, mercaptoguanine derivatives were reported inhibit pyrophosphoryl transfer Staphylococcus aureus (SaHPPK). The present study an attempt understand SaHPPK-inhibitors and...
The Bcl-2 family proteins are the central regulators of apoptosis. Due to its predominant role in cancer progression, act as attractive therapeutic targets. Recently, molecular series Benzothiazole Hydrazone (BH) inhibitors that exhibits drug-likeness characteristics, which selectively targets Bcl-xL have been reported. In present study, docking was used explore plausible binding mode highly active BH inhibitor with Bcl-xL; and Molecular Dynamics (MD) simulation applied investigate stability...
The immunoglobulin heavy chain locus (Igh) features higher-order chromosomal interactions to facilitate stage-specific assembly of the Ig molecule. Cohesin, a ring-like protein complex required for sister chromatid cohesion, shapes chromosome architecture and chromatin important transcriptional regulation often acts together with CTCF. Cohesin is likely involved in B cell activation class switch recombination. Hence, binding profiles cohesin resting mature murine splenic lymphocytes at two...
A detailed comparison of protein domains that belong to families and superfamilies shows structure is better conserved than sequence during evolutionary divergence. Sequence alignments, guided by structural features, permit a sampling the space effective construction libraries for fold recognition. alignments are useful models in defining structure-function relationships superfamilies. The PASS2 database, maintained authors, presents proteins related at superfamily level characterised low...
Myosins are one of the largest protein superfamilies with 24 classes. They have conserved structural features and catalytic domains yet show huge variation at different resulting in a variety functions. molecules driving various kinds cellular processes motility until level organisms. These ATPases that utilize chemical energy released by ATP hydrolysis to bring about conformational changes leading motor function. important as they involved almost all activities ranging from cell division...
Myeloid cell leukemia 1 (Mcl1), is an antiapoptotic member of the Bcl-2 family proteins, has gained considerable importance due to its overexpression activity prevents oncogenic cells undergo apoptosis. This Mcl1 eventually develops strong resistance a wide variety anticancer agents. Therefore, designing novel inhibitors with potentials elicit higher binding affinity and specificity inhibit greater importance. Thus, acts as attractive cancer target. Despite recent experimental advancement in...
Mcl1 is a primary member of the Bcl-2 family-anti-apoptotic proteins (AAP)-that overexpressed in several cancer pathologies. The apoptotic regulation mediated through binding pro-apoptotic peptides (PAPs) (e.g., Bak and Bid) at canonical hydrophobic groove (CBG) Mcl1. Although all PAPs form amphipathic α-helices, their amino acid sequences vary to different degree. This sequence variation exhibits central role partner selectivity towards AAPs. Thus, constructing novel peptide or small...
Profile based sequence search methods are widely used to obtain homologous proteins with the usage of stringent statistical measures. These simple searches, albeit their high sensitivity, cannot solely be relied, while searching for protein families functional diversity and sharing structural similarity other families. Myosins motor that drive cellular mobility associated functions in eukaryotes. motors utilize chemical energy released by ATP hydrolysis bring about conformational changes...
Myeloid cell leukemia-1 (Mcl1) is an anti–apoptotic protein that has gained considerable attention due to its overexpression activity prevents death. Therefore, a potential inhibitor specifically targets Mcl1 with higher binding affinity necessary. Recently, series of N-substituted 1-hydroxy-4-sulfamoyl-2-naphthoate compounds was reported Mcl1, but mechanism remains unexplored. Here, we attempted explore the molecular using advanced computational approaches: pharmacophore-based 3D-QSAR,...
Genomic and transcriptomic data have been generated across a wide range of prostate cancer (PCa) study cohorts. These can be used to better characterize the molecular features associated with clinical outcomes test hypotheses multiple, independent patient In addition, derived features, such as estimates cell composition, risk scores, androgen receptor (AR) develop novel leveraging existing multi-omic datasets. The full potential is yet realized datasets exist in different repositories,...
Genomic and transcriptomic data have been generated across a wide range of prostate cancer (PCa) study cohorts. These can be used to better characterize the molecular features associated with clinical outcomes test hypotheses multiple, independent patient In addition, derived features, such as estimates cell composition, risk scores, androgen receptor (AR) develop novel leveraging existing multi-omic datasets. The full potential is yet realized datasets exist in different repositories,...
Abstract The immunoglobulin (Ig) heavy chain locus comprises several higher order chromosomal interactions to facilitate stage-specific assembly of the Ig molecule. cohesin complex acts together with CTCF regulate long-range chromatin important for transcriptional regulation during cell differentiation. We elucidated binding profile in mature resting and switch-activated B lymphocytes by immuno-precipitation coupled deep sequencing. Comparative genomic analysis revealed specific changes...