Restart procedures for the conjugate gradient method

Powell, M. J. D.

doi:10.1007/bf01593790

Cited by 1,565 publications

(822 citation statements)

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“…Hydrogen atoms were introduced using the CHARMM22 parameter set (Brooks et al, 1983) with electrostatic and van der Waals energy terms enabled using the program X-PLOR (Brünger, 1992), in order to insure energetically reasonable initial positions for the hydrogen atoms. The model was subsequently subjected to 1,000 steps of Powell energy minimization (Powell, 1977).…”

Section: Electrostatic Calculationsmentioning

confidence: 99%

Structure of the Transmembrane Cysteine Residues in Phospholamban

Arkin

Adams

Brünger

et al. 1997

Journal of Membrane Biology

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Abstract. Phospholamban, a 52-residue membrane protein, associates to form a pentameric complex of five long ␣-helices traversing the sarcoplasmic reticulum membrane of cardiac muscle cells. The transmembrane domain of the protein is largely hydrophobic, with only three cysteine residues having polar side chains, yet it functions as a Ca 2+ -selective ion channel. In this report, infrared spectroscopy is used to probe the conformation of the three cysteine side chains and to establish whether the free S-H groups form intrahelical hydrogen bonds in the pentameric complex. Vibrational spectra of a transmembrane peptide were obtained which corresponded to the transmembrane domain of wild-type phospholamban and three peptides each containing a cysteine ⇒ alanine substitution. The observed S-H frequencies argue that each of the sulfhydryl groups is hydrogen-bonded to an i-4 backbone carbonyl oxygen. Electrostatic calculations on a model of phospholamban based on molecular dynamics and mutagenesis studies, show that the sulfhydryl groups may significantly contribute to the electrostatic potential field of the protein.

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Section: Electrostatic Calculationsmentioning

confidence: 99%

Structure of the Transmembrane Cysteine Residues in Phospholamban

Arkin

Adams

Brünger

et al. 1997

Journal of Membrane Biology

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“…This simulated annealing protocol used a van der Waals force constant increasing from 0.003 to 4.000 kcal mol" k 2 . This simulated annealing protocol was followed by a restrained Powell energy minimization (Powell, 1977), including potentials for bonds, angles, impropers, non-bonded LennardJones interactions, electrostatic interactions with a fixed dielectric constant, and square well potentials for the experimentally derived constraints with distance and dihedral force constants at 50 kcal mol" k 2 and 80 kcal mol" rad", respectively. The non-bonded interactions were evaluated with a cutoff of 8.5 A.…”

Section: Methodsmentioning

confidence: 99%

Three‐dimensional solution structure of β cryptogein, a β elicitin secreted by a phytopathogenic fungus phytophthora cryptogea

Fefeu

Bouaziz

et al. 1997

Protein Science

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Cryptogein belongs to a new family of 10-kDa proteins called elicitins. Elicitins are necrotic and signaling proteins secreted by Phytophthora spp. responsible for the incompatible reaction and systemic hypersensitive-like necroses of diverse plant species leading to resistance against fungal or bacterial plant pathogens. The solution structure of /?cryptogein from Phytophthoru cryptogeu fungus was determined by using multidimensional heteronuclear nuclear magnetic resonance spectroscopy. A set of 18 structures was calculated using 1360 NOE-derived distance restraints and 40 dihedral angle restraints obtained from 'JHNHa couplings. The RMS deviation from the mean structure is 0.87 k 0.14 A for backbone atoms and 1.34 2 0.14 A for all the non-hydrogen atoms of residues 2 to 98. The structure of /?cryptogein reveals a novel protein fold, with five helices and a double-stranded /?-sheet facing an R-loop. One edge of the /?-sheet and the adjacent face of the R-loop form a hydrophobic cavity. This cavity made of highly conserved residues represents a plausible binding site. Residue 13, which has been identified from directed mutagenesis and natural sequence comparison studies as a key amino acid involved in the differential control of necrosis, is surface exposed and could contribute to the binding to a ligand or a receptor. The solution structure is close to the X-ray structure, with slight differences lightly due to the crystal packing.

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“…Feedforward supervised network architecture is mostly used with variant of Backpropogation Algorithm to solve the object recognition problems (Gonzalez and Woods, 2002). The literature review suggested that scaled conjugate gradient Algorithm and Conjugate Gradient with Powell/Beale Restart Method Algorithm performs well in object recognition applications (Johansson et al, 1991;Moller, 1993;Powell, 1977;Beale et al, 2010).…”

Section: Artificial Neural Networkmentioning

confidence: 99%