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Biochemistry, ISSN 0006-2960, 10/2008, Volume 47, Issue 40, pp. 10503 - 10512
Journal Article
Journal of Biological Chemistry, ISSN 0021-9258, 01/2012, Volume 287, Issue 1, pp. 58 - 67
Journal Article
Protein Science, ISSN 0961-8368, 12/2002, Volume 11, Issue 12, pp. 2774 - 2791
Methods that predict membrane helices have become increasingly useful in the context of analyzing entire proteomes, as well as in everyday sequence analysis.... 
Av‐Cid, normalized average hydrophobicity scale (Cid 1992) | PSI‐BLAST, position‐specific iterated database search (Altschul et al. 1997) | TrEMBL, translation of the EMBL‐nucleotide database coding DNA to protein sequences (Bairoch and Apweiler 2000) | TopPred2, hydrophobicity‐based membrane helix prediction (von Heijne 1992; Cserzö et al. 1997) | Fauchere, hydrophobic parameter π from the partitioning of N‐acetyl‐amino‐acid amides (Fauchere and Pliska 1983) | BIG, nonidentical merger of SWISS‐PROT (Bairoch and Apweiler 2000) and TrEMBL (Bairoch and Apweiler 2000) and PDB (Berman et al. 2000) | PHDhtm, profile‐based neural network prediction of transmembrane helices (Rost 1996; Rost et al. 1996b) | Eisenberg, normalized consensus hydrophobicity scale (Eisenberg et al. 1984) | TM, transmembrane | MEMSAT, dynamic‐programming based prediction of transmembrane helices (Jones et al. 1994) | PDB, Protein Data Bank of experimentally determined 3D structures of proteins (Bernstein et al. 1977; Berman et al. 2000) | A‐Cid, normalized hydrophobicity scale for α‐proteins (Cid 1992) | GES, hydrophobicity property (Engelman et al. 1986; Prabhakaran 1990) | MaxHom, dynamic programming algorithm for conservation weight‐based multiple sequence alignment (Sander and Schneider 1991) | EM, Solvation free energy (Eisenberg and McLachlan 1986) | bioinformatics | SignalP, signal peptide prediction (Nielsen et al. 1997a) | Ben‐Tal, hydrophobicity scale representing the free energy of transferring an amino acid from water into the center of the hydrocarbon region of a lipid bilayer (Kessel and Ben‐Tal 2002) | TMHMM, transmembrane prediction using cyclic hidden Markov models (Sonnhammer et al. 1998; Krogh et al. 2001) | computational biology | Roseman, solvation‐corrected side‐chain hydropathy (Roseman 1988) | KD, Kyte–Doolittle hydropathy index (Kyte and Doolittle 1982) | PHDpsihtm, divergent profile (PSI‐BLAST)‐based neural network prediction 2002 | Radzicka, transfer free energy from 1‐octanol to water (Radzicka and Wolfenden 1988) | Sweet, optimal matching hydrophobicity (Sweet and Eisenberg 1983) | HMM, hidden Markov model | SWISS‐PROT, database of protein sequences (Bairoch and Apweiler 2000) | TMAP, alignment‐based prediction of transmembrane helices (Persson and Argos 1996) | Wolfenden, hydration potential (Wolfenden et al. 1981) | BLAST, fast sequence alignment method (Altschul and Gish 1996) | Levitt, hydrophobic parameter (Levitt 1976) | multiple alignments, predicting transmembrane helices | proteomes | Lawson, transfer free energy (Lawson et al. 1984) | WW, Wimley–White hydrophobicity scale‐based method (Wimley et al. 1996a,b; White and Wimley 1999; White 2001) | Nakashima, normalized composition of membrane proteins (Nakashima et al. 1990) | SOSUI, hydrophobicity‐ and amphiphilicity‐based transmembrane helix prediction (Hirokawa et al. 1998) | Bull‐Breese, Bull‐Breese hydrophobicity scale (Bull 1974) | SPLIT, transmembrane helix prediction (Juretic et al. 1998) | EVA, server automatically evaluating structure prediction methods (Eyrich et al. 2001a,b) | comparing genomes | TMpred, prediction of transmembrane helices (Hofmann and Stoffel 1993) | Heijne, transfer free energy to lipophilic phase (von Heijne and Blomberg 1979) | TMH, transmembrane helix | HMMTOP, hidden Markov model predicting transmembrane helices (Tusnady and Simon 1998) | Sequence analysis | protein structure prediction | DSSP, program assigning secondary structure (Kabsch and Sander 1983) | META‐PP, internet service allowing access to a variety of bioinformatics tools through one single interface (Eyrich and Rost 2000) | Hopp‐Woods, Hopp‐Woods hydrophilicity value (Hopp and Woods 1981) | Protein structure prediction | Multiple alignments, predicting transmembrane helices | Proteomes | Bioinformatics | Comparing genomes | Computational biology | PROTEIN SECONDARY STRUCTURE | predicting transmembrane helices | BIOCHEMISTRY & MOLECULAR BIOLOGY | ESCHERICHIA-COLI | multiple alignments | ACID SIDE-CHAINS | TOPOLOGY PREDICTION | INTEGRAL MEMBRANE-PROTEINS | BACTERIAL OUTER-MEMBRANE | SARCOPLASMIC-RETICULUM CA2+-ATPASE | STRUCTURAL CLASSIFICATION | sequence analysis | C-TERMINAL DOMAIN | MITOCHONDRIAL PROTEINS | Computational Biology - methods | Algorithms | Animals | Membrane Proteins - chemistry | Protein Structure, Secondary | Sensitivity and Specificity | Models, Molecular | Software | Protein Folding
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 08/2014, Volume 10, Issue 8, pp. 3459 - 3472
An extension of the recently developed PRIMO coarse-grained force field to membrane environments, PRIMO-M, is described. The membrane environment is modeled... 
LIPID-BILAYERS | TRANSMEMBRANE HELICES | GLYCOPHORIN-A | AMINO-ACIDS | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | COMPUTER-SIMULATIONS | IMPLICIT-MEMBRANE | FUSION PEPTIDE | MOLECULAR-DYNAMICS SIMULATIONS | TILT ANGLES | HYDROPHOBIC MISMATCH
Journal Article
Journal Article