Energy functions for protein design

Gordon, Dan; Marshall, Shannon; Mayo, Stephen L.

doi:10.1016/s0959-440x(99)80072-4

Cited by 196 publications

(127 citation statements)

References 33 publications

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“…Bases in DNA may pair by hydrogen bonding, an interaction not accounted for by the RE 2 potential, which is based upon atomic van der Waals interactions. We add this in explicitly using a phenomenological potential with a form generalized from that used in all-atom studies 30 :…”

Section: Sugar-sugar and Sugar-phosphate Van Der Waals Interactionsmentioning

confidence: 99%

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A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality

Morriss-Andrews

Rottler

Plotkin

2010

The Journal of Chemical Physics

117

165

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We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with minimal phenomenology. Persistence length, degree of stacking, and twist are studied by molecular dynamics simulation as functions of temperature, salt concentration, sequence, interaction potential strength, and local position along the chain, for both single-and double-stranded DNA where appropriate. The model of DNA shows several phase transitions and crossover regimes in addition to dehybridization, including unstacking, untwisting, and collapse which affect mechanical properties such as rigidity and persistence length. The model also exhibits chirality with a stable right-handed and metastable left-handed helix.

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Section: Sugar-sugar and Sugar-phosphate Van Der Waals Interactionsmentioning

confidence: 99%

“…This indicates that the decimated stacking pattern we observe for bases is due to frustration between stacking interactions and the other potentials in the model (bond, angle, dihedral). These simulations were done with HET DS, 30 at an ionic concentration of 0.04 mol/L and a temperature of 0.07ǫ.…”

Section: A Persistence Length Of Ssdna and Dsdnamentioning

confidence: 99%

A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality

Morriss-Andrews

Rottler

Plotkin

2010

The Journal of Chemical Physics

117

165

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“…HyPE is designed to calculate the potential of hydrogen bonds formed between the N-H and C = O atoms in the backbone of a protein structure. The calculation of this potential is in accordance with the 12-10 model (Gordon et al 1999). The program will run on a protein data file, with all hydrogen atom positions provided explicitly.…”

Section: Hype: Hydrogen-bond Potential Energy Programmentioning

confidence: 99%

“…2. The equation used for the calculation of the potential energy as described by Gordon et al (Gordon et al 1999) is as follows:…”

Section: Hype: Hydrogen-bond Potential Energy Programmentioning

confidence: 99%

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bPE toolkit: toolkit for computational protein engineering

2014

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We present a computational toolkit consisting of five utility tools, for performing basic operations on a protein structure file in PDB format. The toolkit consists of five different programs which can be integrated as part of a pipeline for computational protein structure characterization or as a standalone analysis package. The programs include tools for chirality check for amino acids (ProChiral), contact map generation (CoMa), data redundancy (DaRe), hydrogen bond potential energy (HyPE) and electrostatic interaction energy (EsInE). All programs in the toolkit can be accessed and downloaded through the following link: http://www.iitg.ac.in/bpetoolkit/.

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Conformational splitting: A more powerful criterion for dead-end elimination

Pierce

Spriet²,

Desmet³

et al. 2000

J. Comput. Chem.

134

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Dead-end elimination (DEE) is a powerful theorem for selecting optimal protein side-chain orientations from a large set of discrete conformations. The present work describes a new approach to dead-end elimination that effectively splits conformational space into partitions to more efficiently eliminate dead-ending rotamers. Split DEE makes it possible to complete protein design calculations that were previously intractable due to the combinatorial explosion of intermediate conformations generated during the convergence process.

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Energy functions for protein design

Cited by 196 publications

References 33 publications

A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality

A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality

bPE toolkit: toolkit for computational protein engineering

Conformational splitting: A more powerful criterion for dead-end elimination

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