Fast learning optimized prediction methodology (FLOPRED) for protein secondary structure prediction.

Abstract:

:Computational methods are rapidly gaining importance in the field of structural biology, mostly due to the explosive progress in genome sequencing projects and the large disparity between the number of sequences and the number of structures. There has been an exponential growth in the number of available protein sequences and a slower growth in the number of structures. There is therefore an urgent need to develop computational methods to predict structures and identify their functions from the sequence. Developing methods that will satisfy these needs both efficiently and accurately is of paramount importance for advances in many biomedical fields, including drug development and discovery of biomarkers. A novel method called fast learning optimized prediction methodology (FLOPRED) is proposed for predicting protein secondary structure, using knowledge-based potentials combined with structure information from the CATH database. A neural network-based extreme learning machine (ELM) and advanced particle swarm optimization (PSO) are used with this data that yield better and faster convergence to produce more accurate results. Protein secondary structures are predicted reliably, more efficiently and more accurately using FLOPRED. These techniques yield superior classification of secondary structure elements, with a training accuracy ranging between 83 % and 87 % over a widerange of hidden neurons and a cross-validated testing accuracy ranging between 81 % and 84 % and a segment overlap (SOV) score of 78 % that are obtained with different sets of proteins. These results are comparable to other recently published studies, but are obtained with greater efficiencies, in terms of time and cost.

journal_name

J Mol Model

authors

Saraswathi S,Fernández-Martínez JL,Kolinski A,Jernigan RL,Kloczkowski A

doi

10.1007/s00894-012-1410-7

subject

Has Abstract

pub_date

2012-09-01 00:00:00

pages

4275-89

issue

9

eissn

1610-2940

issn

0948-5023

journal_volume

18

pub_type

杂志文章
  • Modeling the secondary structures of the peptaibols antiamoebin I and zervamicin II modified with D-amino acids and proline analogues.

    abstract::Antiamoebin I (AAM-I) and zervamicin II (Zrv-IIB) are peptaibols that exert antibiotic activity through the insertion/disruption of cell membranes. In this study, we investigated how the folding of these peptaibols are affected when some of their native residues are replaced with proline analogues and asymmetrical D-α...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-017-3479-5

    authors: Castro TG,Micaêlo NM,Melle-Franco M

    更新日期:2017-10-16 00:00:00

  • Structural and energetic properties of canonical and oxidized telomeric complexes studied by molecular dynamics simulations.

    abstract::The structural and energetic properties of native and oxidized telomeric complexes were defined by means of molecular dynamic (MD) simulations. As a starting point, the experimental conformation of B-DNA d(GpTpTpApGpGpGpTpTpApGpGpG) oligomer bound to human protein telomeric repeat binding factor 1 (TRF1) was used. The...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-013-1859-z

    authors: Czeleń P,Cysewski P

    更新日期:2013-08-01 00:00:00

  • DFT studies on the structural and vibrational properties of polyenes.

    abstract::Detailed density functional theory (DFT) calculations on the structure and harmonic frequencies of model all-trans and all-cis polyenes were undertaken. For the first time, we report on the convergence of selected B3LYP/6-311++G** and BLYP/6-311++G** calculated structural parameters resulting from a systematic increas...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-016-2969-1

    authors: Kupka T,Buczek A,Broda MA,Stachów M,Tarnowski P

    更新日期:2016-05-01 00:00:00

  • In silico characterization of residues essential for substrate binding of human cystine transporter, xCT.

    abstract::xCT is a sodium-independent amino acid antiporter that imports L-cystine and exports L-glutamate in a 1:1 ratio. It is a component of heterodimeric amino acid transporter system Xc- working at the cross-roads of maintaining neurological processes and regulating antioxidant defense. The transporter has 12 transmembrane...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-019-4233-y

    authors: Sharma M,Anirudh CR

    更新日期:2019-11-09 00:00:00

  • In-silico studies on DegP protein of Plasmodium falciparum in search of anti-malarials.

    abstract::Despite encouraging progress over the past decade, malaria caused by the Plasmodium parasite continues to pose an enormous disease burden and is one of the major global health problems. The extreme challenge in malaria management is the resistance of parasites to traditional monochemotherapies like chloroquine and sul...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-016-3064-3

    authors: Sharma D,Soni R,Patel S,Joshi D,Bhatt TK

    更新日期:2016-09-01 00:00:00

  • Theoretical studies on metal porphyrin halides: geometrical parameters and nonlinear optical responses.

    abstract::The geometrical parameters and static electric properties of several metal porphyrin halides, including Fe(III) porphine chloride (FePCl), Fe(III) porphine bromide (FePBr), Fe(III) tetraphenylporphine chloride (FeTPPCl), aluminum phthalocyanine chloride (AlPcCl), gallium(III) phthalocyanine chloride (GaPcCl), and mang...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-009-0556-4

    authors: Asghari-Khiavi M,Safinejad F

    更新日期:2010-03-01 00:00:00

  • First-principles study of the structural transformation, electronic structure, and optical properties of crystalline 2,6-diamino-3,5-dinitropyrazine-1-oxide under high pressure.

    abstract::Periodic first-principles calculations have been performed to study the effect of high pressure on the geometric, electronic, and absorption properties of 2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105) under hydrostatic pressures of 0-50 GPa. Obvious irregular changes in lattice constants, unit-cell angles, bond le...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-013-1995-5

    authors: Wu Q,Yang C,Pan Y,Xiang F,Liu Z,Zhu W,Xiao H

    更新日期:2013-12-01 00:00:00

  • Rational design of carbonitrile-carboxaldehyde cation receptor models: probing the nature of the heteroatom-metal interaction.

    abstract::In this work, hybrid functional and G4 methods were employed in the rational design of carbonitrile-carboxaldehyde receptor models for cation recognition. Electron-sharing and ionic interactions between the models and the cations were analyzed utilizing the concepts of overlap population, atomic valence, electrostatic...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-014-2428-9

    authors: Rosli AN,Abu Bakar MA,Lee VS,Zain SM,Ahmad MR,Abdul Manan NS,Alias Y,Woi PM

    更新日期:2014-09-01 00:00:00

  • Detection of symmetrical decomposition of molecules--isotopomeric analysis of the M/2 clusters.

    abstract::The interpretation of mass spectra (ms) of molecules containing poly-isotopic elements (e.g. Ge, Se, W, Os, Sn, Te, Zn, Yb) can be difficult due to the occurrence of fragments resulting from isotopomeric composition. MS-clusters located in the range lower than or equal to M/2 are very difficult to interpret. In this a...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-009-0486-1

    authors: Goraczko AJ,Szewczykowska K

    更新日期:2009-06-01 00:00:00

  • A molecular mechanics and semiempirical molecular orbital study on the conformation of polynorbornene chains.

    abstract::The conformational analysis of polynorbornene (PNB) chains was investigated with the AM1, MM2, AMBER and OPLS methods taking into consideration the possibility of binding of norbornene monomers to each other at various positions, i.e. exo-exo, exo-endo, endo-endo. The chain that is formed by connecting exo-endo positi...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-003-0139-8

    authors: Yilmaz SS,Abbasoğlu R,Hazer B

    更新日期:2003-08-01 00:00:00

  • Neighboring group stabilization by sigma-holes.

    abstract::We have used density-functional theory to investigate the neighboring-group stabilization of iodine, arsenic, and phosphorus-centered oxyanion moieties in species such as deprotonated 2-iodoxybenzoic acid (IBX) and its analogs. The magnitudes of different stabilizing effects and further candidates for analogous stabil...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-009-0567-1

    authors: O'Hair RA,Williams CM,Clark T

    更新日期:2010-03-01 00:00:00

  • Study of the betulin molecule in a water environment; ab initio and molecular simulation calculations.

    abstract::Ab initio and molecular simulation methods were used in calculations of the neutral individual betulin molecule, and molecular simulations were used to optimize the betulin molecule immersed in various amounts of water. Individual betulin was optimized in different force fields to find the one exhibiting best agreemen...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-011-1055-y

    authors: Pospíšil M,Kovář P,Vácha R,Svoboda M

    更新日期:2012-01-01 00:00:00

  • Conformational analysis of lignin models: a chemometric approach.

    abstract::In the present work, conformational analysis of lignin models was accomplished by considering four cross-link types (3-5', β-5', α-O-4 and β-O-4) and three monomer units [guaiacyl (G), p-hydroxyphenyl (H) and syringyl (S)]. Analysis involving the 3-5' and β-5' dimers was conducted following the standard procedure, i.e...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-012-1689-4

    authors: Castilho-Almeida EW,De Almeida WB,Dos Santos HF

    更新日期:2013-05-01 00:00:00

  • Structures, spectroscopic and thermodynamic properties of U₂On (n = 0 ∼ 2, 4) molecules: a density functional theory study.

    abstract::The equilibrium structures, spectroscopic and thermodynamic parameters [entropy (S), internal energy (E), heat capacity (C p)] of U₂, U₂O, U₂O₂ and U₂O₄ uranium oxide molecules were investigated systematically using density functional theory (DFT). Our computations indicated that the ground electronic state of U₂ is t...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-013-2037-z

    authors: Li P,Niu WX,Gao T,Wang F,Jia TT,Meng DQ,Li G

    更新日期:2013-12-01 00:00:00

  • Identification of novel, less toxic PTP-LAR inhibitors using in silico strategies: pharmacophore modeling, SADMET-based virtual screening and docking.

    abstract::Human leukocyte antigen-related (PTP-LAR) is a receptor-like transmembrane phosphatase and a potential target for diabetes, obesity and cancer. In the present study, a sequence of in silico strategies (pharmacophore mapping, a 3D database searching, SADMET screening, and docking and toxicity studies) was performed to ...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-011-1037-0

    authors: Ajay D,Sobhia ME

    更新日期:2012-01-01 00:00:00

  • Calixarene building block bis(2-hydroxyphenyl)methane (2HDPM) and hydrogen-bonded 2HDPM-H₂O complex in electronic excited state.

    abstract::Intramolecular and intermolecular hydrogen bonding in electronic excited states of calixarene building blocks bis(2-hydroxyphenyl)methane (2HDPM) monomer and hydrogen-bonded 2HDPM-H₂O complex were studied theoretically using the time-dependent density functional theory (TDDFT). Twenty-four stable conformations (12 pai...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-012-1710-y

    authors: Wang S,Hao C,Gao Z,Chen J,Qiu J

    更新日期:2013-04-01 00:00:00

  • Effect of explicit water molecules on ligand-binding affinities calculated with the MM/GBSA approach.

    abstract::We tested different approaches to including the effect of binding-site water molecules for ligand-binding affinities within the MM/GBSA approach (molecular mechanics combined with generalised Born and surface-area solvation). As a test case, we studied the binding of nine phenol analogues to ferritin. The effect of wa...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-014-2273-x

    authors: Mikulskis P,Genheden S,Ryde U

    更新日期:2014-06-01 00:00:00

  • Self-consistent field convergence for proteins: a comparison of full and localized-molecular-orbital schemes.

    abstract::Proteins in the gas phase present an extreme (and unrealistic) challenge for self-consistent-field iteration schemes because their ionized groups are very strong electron donors or acceptors, depending on their formal charge. This means that gas-phase proteins have a very small band gap but that their frontier orbital...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-014-2159-y

    authors: Wick CR,Hennemann M,Stewart JJ,Clark T

    更新日期:2014-03-01 00:00:00

  • Theoretical study of absorption of 2,2,6,6-tetramethylpiperidine-1-oxoammonium cation (TEMPO) on TiO₂(110) rutile surface.

    abstract::We present a theoretical study of the adsorption of 2,2,6,6-tetramethylpiperidine-1-oxoammonium cation (TEMPO) onto the TiO₂(110) surface rutile, investigating its bonding nature, electron properties and structural stability. Based on the results obtained with the PBE0/def2-SVP method, natural bond orbital (NBO) analy...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-014-2149-0

    authors: Nieto-López I,Hernández-García L,Bonilla-Cruz J,Sanchez M

    更新日期:2014-03-01 00:00:00

  • A probable means to an end: exploring P131 pharmacophoric scaffold to identify potential inhibitors of Cryptosporidium parvum inosine monophosphate dehydrogenase.

    abstract::Compound P131 has been established to inhibit Cryptosporidium parvum's inosine monophosphate dehydrogenase (CpIMPDH). Its inhibitory activity supersedes that of paromomycin, which is extensively used in treating cryptosporidiosis. Through the per-residue energy decomposition approach, crucial moieties of P131 were ide...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-020-04663-3

    authors: Omolabi KF,Iwuchukwu EA,Agoni C,Olotu FA,Soliman MES

    更新日期:2021-01-09 00:00:00

  • Calculations of the charge distribution in dodecyltrimethylammonium: a quantum chemical investigation.

    abstract::In this work we report the atomic partial charges evaluated on dodecyltrimethylammonium ion. The values obtained from 17 quantum methods [CHELP, CHELPG, MK, NPA at (HF, LDA, PBE, B3LYP)//6-31G++(d,p) level and APT at B3LYP//6-31G++(d,p)] on the molecule optimised at B3LYP/6-31G++(d,p) level were compared to two semiem...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-009-0620-0

    authors: Minisini B,Chavand S,Barthelery R,Tsobnang F

    更新日期:2010-06-01 00:00:00

  • Rate constant calculations of the C2 + HCN → CCCN+H addition via the Master Equation.

    abstract::The addition of C2 to HCN is of relevant interest in astrochemistry. We studied the pathways of this addition to produce CCCN and estimated its reaction rate using the Master Equation in the circumstellar environment. From the results of this study, it was possible to show that a different pathway in the Surface Poten...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-017-3305-0

    authors: da Silva WB,Albernaz AF,Barreto PR,Correa E

    更新日期:2017-04-01 00:00:00

  • Characterization of adenosine receptor in its native environment: insights from molecular dynamics simulations of palmitoylated/glycosylated, membrane-integrated human A(2B) adenosine receptor.

    abstract::Selective A(2B) receptor antagonists and agonists may play a role in important pathologies such as gastrointestinal, neurological (i.e., Alzheimer disease and dementia) and hypersensitive disorders (i.e., asthma), diabetes, atherosclerosis, restenosis and cancer. Hence, it is regarded as a good target for the developm...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-012-1427-y

    authors: Mansourian M,Madadkar-Sobhani A,Mahnam K,Fassihi A,Saghaie L

    更新日期:2012-09-01 00:00:00

  • Theoretical study of noncovalent interactions in XCN···YO2H (X = F, Cl, Br, I; Y = P, As, Sb) complexes.

    abstract::Noncovalent interactions in XCN···YO2H (X = F, Cl, Br, I; Y = P, As, Sb) complexes were investigated using ab initio calculations at the MP2/aug-cc-pVDZ level of theory. There are four different configurations of these complexes, and the complexes are formed via hydrogen bonds, halogen bonds, π-hole interactions, or d...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-017-3358-0

    authors: Zhao Q

    更新日期:2017-06-01 00:00:00

  • Molecular modeling and biophysical analysis of the c-MYC NHE-III1 silencer element.

    abstract::G-Quadruplex and i-Motif-forming sequences in the promoter regions of several oncogenes show promise as targets for the regulation of oncogenes. In this study, molecular models were created for the c-MYC NHE-III(1) (nuclease hypersensitivity element III(1)) from two 39-base complementary sequences. The NHE modeled her...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-007-0254-z

    authors: Cashman DJ,Buscaglia R,Freyer MW,Dettler J,Hurley LH,Lewis EA

    更新日期:2008-02-01 00:00:00

  • A mixed basis with off-center Gaussian functions for the calculation of the potential energy surfaces for π-stacking interactions: dimers of benzene and planar C₆.

    abstract::A practical mixed basis set was developed to facilitate accurate calculations of potential energy surfaces for π-stacking interactions. Correlation consistent basis sets (cc-PVXZ) were augmented by p-type Gaussian functions placed above and below the planes of C6 moieties. Møller-Plesset (MP2, SCS-MP2) and coupled clu...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-014-2558-0

    authors: Yurtsever E

    更新日期:2015-01-01 00:00:00

  • The electronic structure of the C2H4O...2HF tri-molecular heterocyclic hydrogen-bonded complex: a theoretical study.

    abstract::The geometries of three isomers of the C2H4O...2HF tri-molecular heterocyclic hydrogen-bonded complex were examined through B3LYP/aug-cc-pVDZ calculations. Analysis of structural parameters, determination of CHELPG (charge electrostatic potential grid) intermolecular charge transfer, interpretation of infrared stretch...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-008-0337-5

    authors: de Oliveira BG,Araújo RC,Chagas FF,Carvalho AB,Ramos MN

    更新日期:2008-10-01 00:00:00

  • Modeling the E. coli 4-hydroxybenzoic acid oligoprenyltransferase ( ubiA transferase) and characterization of potential active sites.

    abstract::4-hydroxybenzoate oligoprenyltransferase of E. coli, encoded in the gene ubiA, is an important key enzyme in the biosynthetic pathway to ubiquinone. It catalyzes the prenylation of 4-hydroxybenzoic acid in position 3 using an oligoprenyl diphosphate as a second substrate. Up to now, no X-ray structure of this oligopre...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-004-0197-6

    authors: Bräuer L,Brandt W,Wessjohann LA

    更新日期:2004-12-01 00:00:00

  • Screening of functional monomers and solvents for the molecular imprinting of paclitaxel separation: a theoretical study.

    abstract::The interactions between the template molecule paclitaxel (PTX) and seven functional monomers containing methacrylic acid (MA), acrolein (AC), 4-vinylbenzoic acid (4VA), acrylonitrile (AN), 2-vinylpyridine (2VP), 2,6-bisacrylamide pyridine (BAP) and methyl methacrylate (MM) were systematically investigated adopting th...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-019-4277-z

    authors: Wang L,Yang F,Zhao X,Li Y

    更新日期:2020-01-11 00:00:00

  • Effect of partial atomic charges on the calculated free energy of solvation of poly(vinyl alcohol) in selected solvents.

    abstract::It is well-known that properties of poly(vinyl alcohol) (PVA) in the pure and solution states depend largely on the hydrogen bonding networks formed. In the context of molecular simulation, such networks are handled through the Coulombic interactions. Therefore, a good set of partial atom charges (PACs) for simulation...

    journal_title:Journal of molecular modeling

    pub_type: 杂志文章

    doi:10.1007/s00894-014-2554-4

    authors: Noorjahan A,Choi P

    更新日期:2015-03-01 00:00:00