| scholarly article | Q13442814 |
| P50 | author | Robert L Jernigan | Q59682925 |
| P2093 | author name string | M. Kaplan | |
| I. Bahar | |||
| P2860 | cites work | Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation | Q47627928 |
| Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches | Q47633923 | ||
| Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading | Q52310162 | ||
| Elucidating the folding problem of helical peptides using empirical parameters | Q52376869 | ||
| A thermodynamic scale for the beta-sheet forming tendencies of the amino acids | Q53709834 | ||
| Thermodynamic beta-sheet propensities measured using a zinc-finger host peptide | Q54269563 | ||
| Side-Chain Determinants of .beta.-Sheet Stability | Q57823374 | ||
| Context-dependent secondary structure formation of a designed protein sequence | Q59055217 | ||
| Measurement of the β-sheet-forming propensities of amino acids | Q59069627 | ||
| Context is a major determinant of β-sheet propensity | Q59069633 | ||
| Positional independence and additivity of amino acid replacements on helix stability in monomeric peptides | Q67290878 | ||
| Alpha-helix stability in proteins. I. Empirical correlations concerning substitution of side-chains at the N and C-caps and the replacement of alanine by glycine or serine at solvent-exposed surfaces | Q67559626 | ||
| Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force | Q68363646 | ||
| Side chain contributions to the stability of alpha-helical structure in peptides | Q68598333 | ||
| A mutant T4 lysozyme (Val 131----Ala) designed to increase thermostability by the reduction of strain within an alpha-helix | Q68754537 | ||
| Structure-based thermodynamic scale of alpha-helix propensities in amino acids | Q71714553 | ||
| Importance of environment in determining secondary structure in proteins | Q72266480 | ||
| Hydrogen bond strength and beta-sheet propensities: the role of a side chain blocking effect | Q72511006 | ||
| Development of pseudoenergy potentials for assessing protein 3-D-1-D compatibility and detecting weak homologies | Q72777487 | ||
| Structural basis of amino acid alpha helix propensity | Q27732169 | ||
| Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins | Q27860987 | ||
| The Protein Data Bank: a computer-based archival file for macromolecular structures | Q27860989 | ||
| A simplified representation of protein conformations for rapid simulation of protein folding | Q28269973 | ||
| Energy functions that discriminate X-ray and near native folds from well-constructed decoys | Q28278562 | ||
| Amino acid preferences for specific locations at the ends of alpha helices | Q29618508 | ||
| The complexity and accuracy of discrete state models of protein structure | Q30418649 | ||
| Reduced representation model of protein structure prediction: statistical potential and genetic algorithms | Q30422972 | ||
| Coordination geometry of nonbonded residues in globular proteins | Q33368037 | ||
| Side-chain entropy opposes alpha-helix formation but rationalizes experimentally determined helix-forming propensities | Q33611710 | ||
| Knowledge-based prediction of protein structures and the design of novel molecules | Q34183412 | ||
| Rules for alpha-helix termination by glycine | Q34340813 | ||
| Stabilization of lambda repressor against thermal denaturation by site-directed Gly----Ala changes in alpha-helix 3. | Q38350564 | ||
| Adding backbone to protein folding: why proteins are polypeptides | Q41394310 | ||
| Alpha-helix stability in proteins. II. Factors that influence stability at an internal position | Q41949296 | ||
| Pseudodihedrals: simplified protein backbone representation with knowledge-based energy | Q42844377 | ||
| Amino acid similarity coefficients for protein modeling and sequence alignment derived from main-chain folding angles | Q43994343 | ||
| A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids | Q44211659 | ||
| Conformational preferences of amino acids in globular proteins | Q44870543 | ||
| Relative helix-forming tendencies of nonpolar amino acids | Q46587484 | ||
| Protein folding. Effect of packing density on chain conformation | Q46927963 | ||
| P433 | issue | 3 | |
| P407 | language of work or name | English | Q1860 |
| P921 | main subject | computational science | Q117801 |
| protein secondary structure | Q904984 | ||
| P304 | page(s) | 292-308 | |
| P577 | publication date | 1997-11-01 | |
| P1433 | published in | Proteins | Q7251514 |
| P1476 | title | Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches | |
| P478 | volume | 29 |
| Q34262440 | A model-structure of a periplasm-facing state of the NhaA antiporter suggests the molecular underpinnings of pH-induced conformational changes |
| Q34101699 | Biophysical and structural considerations for protein sequence evolution |
| Q30495061 | C(alpha)-trace model of the transmembrane domain of human copper transporter 1, motion and functional implications |
| Q30430358 | Capturing native/native like structures with a physico-chemical metric (pcSM) in protein folding |
| Q35606699 | Coarse-grained molecular dynamics simulations of a rotating bacterial flagellum |
| Q47625877 | Coarse-grained simulations of conformational dynamics of proteins: Application to apomyoglobin |
| Q41790483 | Composites of local structure propensities: Evidence for local encoding of long-range structure |
| Q30489757 | Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase |
| Q41039362 | Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes |
| Q38305067 | Conserved C-terminal nascent peptide binding domain of HYPK facilitates its chaperone-like activity |
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| Q41005043 | Distributions of experimental protein structures on coarse-grained free energy landscapes. |
| Q36280764 | Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions |
| Q30476762 | Exploring global motions and correlations in the ribosome |
| Q41142772 | Features of large hinge-bending conformational transitions. Prediction of closed structure from open state |
| Q30403868 | Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models. |
| Q33195458 | Interactions of hydrophobic peptides with lipid bilayers: Monte Carlo simulations with M2delta |
| Q42106279 | Intrinsic α-helical and β-sheet conformational preferences: a computational case study of alanine. |
| Q41749807 | Knowledge-based entropies improve the identification of native protein structures. |
| Q43053284 | Linking 3D and 2D binding kinetics of membrane proteins by multiscale simulations. |
| Q30407110 | LoCo: a novel main chain scoring function for protein structure prediction based on local coordinates |
| Q36130927 | Molecular determinants of cadherin ideal bond formation: Conformation-dependent unbinding on a multidimensional landscape. |
| Q42232921 | Monte Carlo simulations of peptide-membrane interactions with the MCPep web server |
| Q40324007 | Monte Carlo studies of folding, dynamics, and stability in alpha-helices |
| Q42039279 | Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models |
| Q36631429 | On the properties and sequence context of structurally ambivalent fragments in proteins |
| Q36519520 | Orientational potentials extracted from protein structures improve native fold recognition |
| Q30385764 | Potentials 'R' Us web-server for protein energy estimations with coarse-grained knowledge-based potentials |
| Q43152697 | Propensities, probabilities, and the Boltzmann hypothesis |
| Q47625148 | Recognition of native structure from complete enumeration of low-resolution models with constraints |
| Q34182245 | Structure-based prediction of potential binding and nonbinding peptides to HIV-1 protease |
| Q40579871 | The Transmembrane Helix Tilt May Be Determined by the Balance between Precession Entropy and Lipid Perturbation |
| Q37399868 | The energy profiles of atomic conformational transition intermediates of adenylate kinase |
| Q47959485 | Understanding the Functional Roles of Multiple Extracellular Domains in Cell Adhesion Molecules with a Coarse-Grained Model |
| Q48137432 | W-Band pulse EPR distance measurements in peptides using Gd3+–dipicolinic acid derivatives as spin labels |
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