• His research spans a wide range, from the quantum chemistry of small molecules and the spectroscopic properties of proteins, to the application of state-of-the-art statistical and computer science methodology to problems in bioinformatics, drug design and sustainable chemistry. (nottingham.ac.uk)
  • Structure and properties of proteins, nucleic acids, and their complexes. (keywen.com)
  • The course covers both the principles that determine the properties of proteins and the experimental methods that are used to study these properties in modern molecular protein science. (lu.se)
  • The links to the Web sites in the following list focus on protein sequences. (dummies.com)
  • Protein design methods use trial and error or more sophisticated methods like directed evolution or inverse folding to generate novel scaffolds or to find novel protein sequences folding into a defined scaffold, respectively. (hindawi.com)
  • Given the intimate relationship between a protein's structure and function, a way to design proteins with targeted properties is to start from a desired structure and find sequences able to fold into it, imposing additional constraints in the process [ 1 ]. (hindawi.com)
  • First, the sequences carrying point mutations are modeled on a given template structure, and subsequently, molecular dynamics simulations are carried out for 10 ns. (hindawi.com)
  • Several mutations in the N terminus of the G-protein-coupled receptor rhodopsin disrupt NXS/T consensus sequences for N-linked glycosylation (located at N2 and N15) and cause sector retinitis pigmentosa in which the inferior retina preferentially degenerates. (jneurosci.org)
  • 9 Although there exists sequences homologous to the ORF10 protein in other closely related bat and pangolin CoVs, there are no experimentally derived crystallographic structures for the ORF10 protein. (biorxiv.org)
  • We show the networks generalize by adapting them to variant activity prediction from sequences only, with results that are comparable to a state-of-the-art variant predictor that uses evolutionary and structurally derived features. (biorxiv.org)
  • A yeast-based model system for cloning secreted and membrane proteins. (mpg.de)
  • Aquaporins (AQPs) are small (21-34 kD) integral membrane proteins, which form channels facilitating movement of water and other small solutes across the cell membrane. (biomedcentral.com)
  • Native membrane derived polymer-supported lipid bilayers (nSLBs) are poised to bridge the gap between live cell experiments and traditional model membrane architectures that by offering a combination of accessibility by surface sensitive analytical instrumentation and a composition which more closely resembles cellular membranes by displaying a diversity of endogenous membrane proteins, lipids, and carbohydrates. (lu.se)
  • In convergent evolution, nonhomologous proteins evolve in separate biological contexts to catalyze the same or similar reactions. (hindawi.com)
  • rium properties, completely determined by the interactions within crystal structures of 38 nonhomologous proteins, we find that it the system. (lu.se)
  • Microbial rhodopsins (Rhs) are transmembrane proteins that utilize light-induced isomerization of their retinal cofactor to function as light-sensitive ion channels, pumps and sensors. (elifesciences.org)
  • This new approach has been shown to preserve mobility and enzymatic activity of transmembrane proteins in the resulting nSLB. (lu.se)
  • Rational design of protein structure, activity, and stability. (keywen.com)
  • One of the methods that have been proposed is a multiobjective optimization, in which protein stability and catalytic activity are simultaneously optimized [ 4 , 5 ]. (hindawi.com)
  • Several methods have been proposed to design novel stable proteins, such as multi-objective optimization, in which protein stability and catalytic activity are simultaneously optimized. (hindawi.com)
  • Computational modeling of protein mutant stability: analysis and optimization of statistical potentials and structural features reveal insights into prediction model development. (brenda-enzymes.org)
  • Structural Analysis and Prediction of Protein Mutant Stability using Distance and Torsion Potentials: Role of Secondary Structure and Solvent Accessibility. (brenda-enzymes.org)
  • CUPSAT: prediction of protein stability upon point mutations. (brenda-enzymes.org)
  • Both studies suggest that defects in rhodopsin glycosylation are associated with impairment of protein folding or stability. (jneurosci.org)
  • However, these same mutations do not inflict significant changes on protein stability and other biochemical features. (biorxiv.org)
  • For this purpose, we developed and validated an annotation method (called pairwise comparative modelling) on the basis of a three-dimensional structure (homology comparative modelling), leading to the prediction of 6,095 ARDs in a catalogue of 3.9 million proteins from the human intestinal microbiota. (nature.com)
  • To predict ARDs in the intestinal microbiota, we developed a method based on protein homology modelling (see Methods) that we termed pairwise comparative modelling (PCM). (nature.com)
  • A program for homology protein structure modeling by satisfaction of spatial restraints. (keywen.com)
  • However, analogous proteins may have structural homology although this is not a prerequisite. (hindawi.com)
  • There is a strong emphasis on the structure of molecules, particularly proteins, which are the nanoscale machines that carry out most processes in living organisms. (bbk.ac.uk)
  • Structure: an assortment of carbon molecules in a non-crystalline, irregular, glassy state. (keywen.com)
  • KGNMOL, ab initio electronic structure calculations for large molecules. (keywen.com)
  • The structure of the molecules can be incorporated in the alignment. (keywen.com)
  • Furthermore, one will need to be able to predict the structure patterns generated during the self-organization of whole layers of (bio)molecules on the surface. (degruyter.com)
  • But just as it had originally been the case in other fields of synthetic chemistry, such as molecular or solid state chemistry, the outcome of such a deposition with respect to the structure of the individual molecule or the structural arrangement of many molecules is very hard to predict without prior experimental input. (degruyter.com)
  • But we are still far away from an unbiased structure prediction of thermodynamically and/or kinetically stable structures of molecules on surfaces. (degruyter.com)
  • Similarly, the powerful global search techniques that have been applied to, and sometimes specifically developed for, the structure prediction of crystals and single molecules in vacuum or solvent can also be employed for the prediction of the structure(s) of molecules on surfaces. (degruyter.com)
  • On aver- comprising some 1015 protein molecules. (lu.se)
  • An effective computational method incorporating multiple secondary structure predictions in topology determination for cryo-EM images. (odu.edu)
  • Computational design of novel proteins with well-defined functions is an ongoing topic in computational biology. (hindawi.com)
  • In this review, we present an overview over the current state of the art regarding the prediction and clarification of structures of biomolecules on surfaces using theoretical and computational methods. (degruyter.com)
  • It was on that occasion that in a conversation with David Moss, Professor of Biomolecular Structures, and his co-worker Dr. Clare Sansom, the idea was conceived to organize the postgraduate course in bioinformatics, this newly emerging interdisciplinary research area as the interface between biological and computational sciences, primarily aimed at research students from Central and Eastern Europe. (iospress.nl)
  • Insights from the work on formamide and other small amides have been applied to studies of proteins and have led to significant improvements in the calculation of the circular dichroism of proteins from first principles. (nottingham.ac.uk)
  • His calculations on protein circular dichroism spectroscopy, a key technique in structural biology, are the most accurate to be published. (nottingham.ac.uk)
  • The chosen application is finding fractions of secondary structures of proteins from circular dichroism (CD) spectra employing singular value decomposition, SVD, to obtain the matrix B and its pseudo-reciprocal. (scirp.org)
  • Cysteine-Selective Modification of Peptides and Proteins via Desulfurative C-C Bond Formation CHEMISTRY-A EUROPEAN JOURNAL. (nottingham.ac.uk)
  • This new protein product was discovered serendipitously during a systematic search of potential antigenic peptides recognized by CD8+ T lymphocytes encoded by influenza virus A/Puerto Rico/8/34 (H1N1) ( 4 ). (cdc.gov)
  • We designed new peptides of GRA6, GRA7, and SAG1 proteins, with more SNPs among the three clonal strains than those previously designed. (frontiersin.org)
  • then we designed peptides with linkers joining the specific regions and predicted their 3D structure. (frontiersin.org)
  • developed a typing method based on antibody binding to polymorphic peptides, designed from proteins related to virulence. (frontiersin.org)
  • Ranjan, D. "Improving Protein Secondary Structure Prediction using 3-dimensional Spatial Constraints of the Protein" $122,000. (odu.edu)
  • Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. (keywen.com)
  • Another aspect of Hirst's research focuses on the study of protein-ligand interactions, using techniques including QSAR, machine learning, neural networks, docking, molecular dynamics (MD) simulations and quantum chemistry. (nottingham.ac.uk)
  • The described setup and experimental design enable real-time monitoring of substrate turnover in light-activated enzymes on a molecular scale, thus opening the pathway to a deeper understanding of enzyme activity and protein-protein interactions. (elifesciences.org)
  • Hydrophobicity was one of the most important physicochemical properties, due to the fact that it is involved in protein interactions, for example, by forming hydrophobic cores. (hindawi.com)
  • For example, the 3a protein was shown to induce apoptosis whereas the 9b and 9c proteins were suggested to be involved in membrane interactions during virion assembly and host-virus interactions, respectively. (biorxiv.org)
  • Influenza A virus has eight segments of negative-stranded RNA genome and encodes 10 viral proteins ( 3 ). (cdc.gov)
  • Upstream of the 3'-untranslated region in the SARS-CoV-2 genome is ORF10 which has been proposed to encode for the ORF10 protein. (biorxiv.org)
  • however, the genes encoding for these proteins are maintained in the coronavirus (CoV) genome, suggesting they might play important roles within the environment of the infected host. (biorxiv.org)
  • VH is derived from a single protein domain of 35 residues [ 9 ]. (hindawi.com)
  • Thus, a comprehensive understanding of the activation and inactivation of these novel proteins is of utmost interest. (elifesciences.org)
  • The mdxvu program is a molecular dynamics and molecular structure analysis code. (keywen.com)
  • While many studies have been focused on the membrane structure, the dynamics of such systems are crucial for the function of the membrane including membrane bound proteins. (lu.se)
  • These techniques are replacing x-ray crystallography for the determination of protein structure. (keywen.com)
  • Forum for 3D macromolecular structure determination. (keywen.com)
  • Structure determination and refinement of human alpha class glutathione transferase A1-1. (keywen.com)
  • Advanced spectroscopic techniques for structure and determination in organic chemistry . (keywen.com)
  • Crystal and molecular structure determination. (keywen.com)
  • This protein also possesses high residue protein-binding propensity, primarily in the N-terminal half. (biorxiv.org)
  • Machine learning for yield prediction for chemical reactions using in situ sensors JOURNAL OF MOLECULAR GRAPHICS & MODELLING. (nottingham.ac.uk)
  • Structure is a framework for two-dimensional molecular visualization written in Java and based on Octet. (keywen.com)
  • HQSAR Hologram QSAR (HQSAR) uses molecular holograms and PLS to generate fragment-based structure-activity relationships. (keywen.com)
  • SciVision - Databases , molecular modeling , and structure-activity relationship software for Windows. (keywen.com)
  • The Proceedings of this conference have recently been published in the Journal of Molecular Structure (THEOCHEM) vol 368. (keywen.com)
  • The optimization was guided by directed evolution based on hydrophobicity scores, molecular weight, and secondary structure predictions. (hindawi.com)
  • However, molecular weight is also important due to potential steric incompatibilities within protein cores. (hindawi.com)
  • The molecular approach of using Geneious Prime software and protein prediction data base for characterization of bacteriocin is novel and predicts " KSSAYSLQMGATAIKQVKKLFKKWGW " as peptide responsible for antimicrobial activity. (researchsquare.com)
  • The predicted model suggests the ORF10 protein contains a β-α-β motif with a β-molecular recognition feature occurring in the first β-strand. (biorxiv.org)
  • Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. (rostlab.org)
  • Towards designing modular recurrent neural networks in learning protein secondary structures. (yasni.de)
  • A dynamic programming algorithm for finding the optimal placement of a secondary structure topology in Cryo-EM data. (odu.edu)
  • Abstract The algorithm based on combination learning usually is superior to a single classification algorithm on the task of protein secondary structure prediction. (techscience.com)
  • Protein secondary structure prediction using GOR IV and PSIPRED. (linuxlinks.com)
  • Influenza A virus contains eight RNA segments and encodes 10 viral proteins. (cdc.gov)
  • However, an 11th influenza A viral protein was recently found. (cdc.gov)
  • Unlike other influenza A viral proteins, this novel protein has several unusual features. (cdc.gov)
  • However, the development of reliable HDV RNA assays is challenged by viral heterogeneity (at least 8 different genotypes and several subgenotypes), intra-host viral diversity, rapid viral evolution, and distinct secondary structure features of HDV RNA. (cdc.gov)
  • In addition, some recent works such as [ 19 , 20 ] adopted structural information in other bioinformatics fields and the considerable performance gains indicate the huge potential of protein structural information. (biomedcentral.com)
  • After the spectroscopic characterization of the late rhodopsin photoproducts, we analyzed truncated variants and revealed the involvement of the cytosolic N-terminus in the structural rearrangements upon photo-activation of the protein. (elifesciences.org)
  • Here we use ensembles of bidirectional recurrent neural network architectures, PSI-BLAST-derived profiles, and a large nonredundant training set to derive two new predictors: (a) the second version of the SSpro program for secondary structure classification into three categories and (b) the first version of the SSpro8 program for secondary structure classification into the eight classes produced by the DSSP program. (rostlab.org)
  • Protein structure evaluation showed a hydrophilic aromatic/arginine (ar/R) selectivity filter (SF) in PIPs whereas other subfamilies mostly contained a hydrophobic ar/R SF. (biomedcentral.com)
  • Results indicate a highly ordered, hydrophobic, and thermally stable protein that contains at least one transmembrane region. (biorxiv.org)
  • 12 This protein is hydrophobic with the α-helix having been identified as a possible transmembrane (TM) helix as well. (biorxiv.org)
  • Sulfhydryl Reactivity and Transducin Activation Reveal a Tertiary Structure. (cmu.edu)
  • Reactivity of the Sulfhydryl Groups and their Derivatives Identifies a Tertiary Structure that Changes Upon Light-Activation. (cmu.edu)
  • Herein, this study uses multiple bioinformatic tools to biochemically and functionally characterize the ORF10 protein, along with predicting its tertiary structure. (biorxiv.org)
  • The subcellular localization of EZH2 protein was predicted by using different predictors (CELLO, Euk-mPLoc, WoLF PSORT, and TargetP). (hindawi.com)
  • Fragment libraires improved the accuracy of protein folding and outperformed state-of-the-art algorithms with respect to predicted properties, such as torsion angles and inter-residue distances. (biomedcentral.com)
  • Based on the described research achievements, now we open the protein secondary structure prediction website, for the aim of improving the research communication and international technology service in Internet which concludes providing protein secondary structure predicting results free, receiving academic discussion and improving scientific research level. (predictioncenter.org)
  • Due to the lack of detergent solubilization and reconstitution steps, the nSLBs created using this approach contain essentially all of the native lipids, as well as the membrane-associated proteins and carbohydrates from the donor membrane. (lu.se)
  • Oxidant damage to cellular DNA, proteins (including the epigenome), and lipids can occur when reactive oxygen species escape cell antioxidant and repair mechanisms. (who.int)
  • Ranjan, D. "Phylogenetic predictions of the capabilities of novel biothreat agents" $135,000. (odu.edu)
  • Phylogenetic analysis showed similar numbers of AQPs clustered in five distinct subfamilies including the plasma membrane intrinsic proteins (PIPs), the tonoplast intrinsic proteins (TIPs), the nodulin 26-like intrinsic proteins (NIPs), the small basic intrinsic proteins (SIPs), and the uncharacterized intrinsic proteins (XIPs). (biomedcentral.com)
  • It imports hundreds of nucleus-encoded proteins, and diverse metabolites are continuously exchanged across the two chromatophore envelope membranes. (frontiersin.org)
  • A mechanism for stabilization of membranes at low temperatures by an antifreeze protein. (mpg.de)
  • Mounting evidence suggests that the genetic disorders/mutation and diseases change not only the protein expression patterns but also membranes themselves. (lu.se)
  • Found upstream of the 3'-untranslated region (3'-UTR), ORF10 (117 nt long) encodes for a protein that is 38 amino acids in length. (biorxiv.org)
  • In ICM, the amino acid sequence of the target was tethered to the parent structure. (keywen.com)
  • Together, these results indicate that the structure of the rhodopsin N terminus must be maintained by an appropriate amino acid sequence surrounding N2 and may require a carbohydrate moiety at N15. (jneurosci.org)
  • In response to the presence of certain activating substances, including oxidized LDL, monocyte chemoattractant protein 1 (MCP-1), interleukin (IL)-8, and platelet-derived growth factor (PDGF), leukocytes migrate into the wall of the artery (see the image below). (medscape.com)
  • The alpha granules contain hemostatic proteins such as fibrinogen, vWf, and growth factors (eg, platelet-derived growth factor and transforming growth factors). (medscape.com)
  • Such features, when coupled with carefully designed algorithms, lead to good predictions empirically. (biomedcentral.com)
  • Ranjan, D. "ABI Innovation: Advanced Informatics and Eective Algorithms for Improved CryoEM Protein Structure Prediction and Density Analysis" $589,703. (odu.edu)
  • Adequate test problems are those which simulate the real database and demonstrate or quantify the prediction capability of the algorithms employed. (scirp.org)
  • It also includes the study of existing drugs, their biological properties, and their quantitative structure-activity relationships (QSAR). (keywen.com)
  • Sensitive quantitative detection of disease-related proteins is critical to many areas of modern biochemical and biomedical research. (cdc.gov)
  • N-linked glycosylation is the most prevalent posttranslational modification of plasma membrane and secretory proteins and participates in many important biological roles such as protein folding, intracellular targeting, immune response, cell adhesion, and protease resistance. (jneurosci.org)
  • We broadened the usage of such structural information by transforming fragment libraries into protein-specific potentials for gradient-descent based protein folding and encoding fragment libraries as structural features for protein property prediction. (biomedcentral.com)
  • Given that the energy potentials are mainly derived from the predicted protein properties, the accuracy of the predicted protein properties, to a large extent, determines the quality of final predicted structures. (biomedcentral.com)
  • A total of five major Open Reading Frames (ORF) were found in COVID-19: the ORF 1a/b region coding replicase and other enzymes, the spike or S protein ORF, M or membrane glycoprotein ORF, E or small membrane protein ORF and the N or nucleocapsid ORF ( fig. 1 )[ 5 ]. (ijpsonline.com)
  • 2 In particular, the 3'-terminus encompasses multiple open reading frames (ORFs) that encode four main structural proteins: the spike (S), membrane (M), envelope (E), and nucleocapsid (N) proteins. (biorxiv.org)
  • establish mechanisms of action by studying the effects of the same chemicals in experimental animals and on human cells in vitro, allowing for a better prediction of human carcinogenicity and assessment of carcinogenic mechanisms. (who.int)
  • We proposed a novel electrochemical immunosensor for sensitive detection of cancer biomarker alpha-fetoprotein (AFP) using a graphene sheets sensor platform and functionalized carbon nanospheres (CNS) labeling with horseradish peroxidase-secondary antibodies (HRP-Ab2). (cdc.gov)
  • Ensemble Voting System for Multiclass protein fold Recognition. (vldb.org)
  • Ensemble of Probabilistic Neural Networks for Protein Fold Recognition. (vldb.org)
  • As an unintended consequence, this putatively encoded protein within SARS-CoV-2 has remained somewhat understudied. (biorxiv.org)
  • Initially the problem was attacked using the techniques that were current, namely constructing the spectral functions describing secondary structures presumed to be present and responsible for the CD spectra. (scirp.org)
  • Deriving protein secondary structure content from CD spectra has changed from postulating component spectra of the characteristic structures to the use of the secondary structure fractions from X-ray data as a basis for the mathematical prediction of the component spectra representation of the CD database. (scirp.org)
  • Protein secondary structure prediction based on position-specific scoring matrices. (keywen.com)
  • Here we show by mass spectrometric analyses of enriched insoluble protein fractions that, unexpectedly, nucleus-encoded transporters are not inserted into the chromatophore inner envelope membrane. (frontiersin.org)
  • The database noise spectrum can be used to prepare the reduced noise CD spectrum for a new protein to yield its structural fractions and their uncertainties. (scirp.org)
  • Rarely are the fractions of secondary structures reported with the concomitant standard deviations or is the experimental error associated with the resulting functional fitting to the CD spectrum available. (scirp.org)
  • Together, the human disease and animal models suggest that glycosylation plays a crucial role in the structure and/or function of rhodopsin. (jneurosci.org)
  • Predicting the secondary structure from protein sequence plays a crucial role in estimating the 3D structure, which has applications in drug design and in understanding the function of proteins. (agu.edu.tr)
  • proteins could carry out their biological functions. (lu.se)
  • Secondary structure predictions are increasingly becoming the workhorse for several methods aiming at predicting protein structure and function. (rostlab.org)
  • Structure-function relationships in metalloenzyme mimics. (keywen.com)
  • EnzymeDetector: an integrated enzyme function prediction tool and database. (brenda-enzymes.org)
  • The general aim of the course is to enable students to acquire an advanced understanding of proteins with an emphasis on their three-dimensional structures, the connection of structures to biological function and how these structures are produced. (lu.se)
  • Structure and relation to Function. (lu.se)
  • Mutations affecting glycosylation of the heptahelical G-protein-coupled receptor rhodopsin are associated with retinitis pigmentosa (RP), a disease characterized by progressive degeneration of photoreceptors. (jneurosci.org)
  • In this work, we generated and optimized a new synthetic fusion protein using an evolutionary approach. (hindawi.com)
  • Learning the natural distribution of evolutionary protein sequence variation is a logical step toward predictive and generative modeling for biology. (biorxiv.org)
  • larger amplitude are sampled and do not converge even in nano- about protein flexibility has come from x-ray crystallography, in the second-length simulations (8, 9). (lu.se)
  • Furthermore, chromatophore-localized biosynthetic pathways as well as multiprotein complexes include proteins of dual genetic origin, suggesting that mechanisms evolved that coordinate gene expression levels between chromatophore and nucleus. (frontiersin.org)
  • As one of the two distinct complexes, namely, Polycomb Repressive Complex 1 (PRC1) and PRC2, PRC2 mediates gene silencing by modulating chromatin structure [ 2 ]. (hindawi.com)