| scholarly article | Q13442814 |
| P2093 | author name string | B Honig | |
| A Windemuth | |||
| N Froloff | |||
| P2860 | cites work | Entropic Contributions to Rate Accelerations in Enzymic and Intramolecular Reactions and the Chelate Effect | Q24617542 |
| Crystal structures of two viral peptides in complex with murine MHC class I H-2Kb | Q27642080 | ||
| The antigenic identity of peptide-MHC complexes: a comparison of the conformations of five viral peptides presented by HLA-A2 | Q27729917 | ||
| Crystal structure of an H-2Kb-ovalbumin peptide complex reveals the interplay of primary and secondary anchor positions in the major histocompatibility complex binding groove | Q27729958 | ||
| The interpretation of protein structures: Estimation of static accessibility | Q27860750 | ||
| Free R value: a novel statistical quantity for assessing the accuracy of crystal structures | Q27860894 | ||
| The Protein Data Bank: a computer-based archival file for macromolecular structures | Q27860989 | ||
| Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons | Q27861091 | ||
| Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects | Q28271916 | ||
| Free energy determinants of secondary structure formation: I. alpha-Helices | Q28289702 | ||
| Free energy determinants of secondary structure formation: II. Antiparallel beta-sheets | Q28289711 | ||
| Areas, volumes, packing and protein structure | Q28294108 | ||
| On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5. | Q30195996 | ||
| Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis | Q30403890 | ||
| Hydrogen bond stereochemistry in protein structure and function | Q30412768 | ||
| The statistical-thermodynamic basis for computation of binding affinities: a critical review | Q33915676 | ||
| Hydrogen bonding stabilizes globular proteins | Q34040782 | ||
| A free energy analysis of nucleic acid base stacking in aqueous solution | Q34047381 | ||
| Functional group contributions to drug-receptor interactions. | Q34245543 | ||
| The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure | Q34326042 | ||
| Computational methods to predict binding free energy in ligand-receptor complexes | Q34369739 | ||
| Empirical scale of side-chain conformational entropy in protein folding | Q34731368 | ||
| Side-chain conformational entropy in protein folding | Q34732367 | ||
| Toward an estimation of binding constants in aqueous solution: studies of associations of vancomycin group antibiotics | Q36094033 | ||
| Peptide-induced conformational changes in class I heavy chains alter major histocompatibility complex recognition | Q36232028 | ||
| Major histocompatibility complex conformational epitopes are peptide specific | Q36232104 | ||
| Analysis of the structure of empty and peptide-loaded major histocompatibility complex molecules at the cell surface | Q36364026 | ||
| Alloantibodies can discriminate class I major histocompatibility complex molecules associated with various endogenous peptides | Q36441789 | ||
| Ranking potential binding peptides to MHC molecules by a computational threading approach | Q36678734 | ||
| Prominent role of secondary anchor residues in peptide binding to HLA-A2.1 molecules | Q36741865 | ||
| Electrostatic interactions in macromolecules: theory and applications | Q37938174 | ||
| Free energy via molecular simulation: applications to chemical and biomolecular systems | Q38648060 | ||
| Computer-aided molecular design | Q39671687 | ||
| Co-operativity in protein-protein association. The structure and stability of the actin filament | Q39782107 | ||
| Protein-peptide interactions | Q40540879 | ||
| Biophysical tools for structure-based drug design | Q40667170 | ||
| Peptide-induced conformational change of the class I heavy chain | Q41683551 | ||
| Binding of phosphorus-containing inhibitors to thermolysin studied by the Poisson-Boltzmann method | Q42844649 | ||
| Computational method for relative binding energies of enzyme-substrate complexes | Q42845172 | ||
| Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches | Q46798591 | ||
| Peptide-induced conformational changes in class I molecules. Direct detection by flow cytometry. | Q50119803 | ||
| A continuum model for protein-protein interactions: application to the docking problem. | Q52336008 | ||
| The contribution of vibrational entropy to molecular association. The dimerization of insulin. | Q52377208 | ||
| In vitro peptide binding to soluble empty class I major histocompatibility complex molecules isolated from transfected Drosophila melanogaster cells. | Q52441433 | ||
| 23 Theoretical calculations of relative affinities of binding | Q52464273 | ||
| CHARMM: A program for macromolecular energy, minimization, and dynamics calculations | Q53340989 | ||
| Evaluation of the conformational free energies of loops in proteins. | Q54641591 | ||
| Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison | Q57000556 | ||
| Free Energy of Amide Hydrogen Bond Formation in Vacuum, in Water, and in Liquid Alkane Solution | Q57207152 | ||
| Effect of Conformational Flexibility and Solvation on Receptor-Ligand Binding Free Energies | Q58489284 | ||
| Calculation of the relative change in binding free energy of a protein-inhibitor complex | Q69736806 | ||
| Calculation of the electric potential in the active site cleft due to alpha-helix dipoles | Q72952190 | ||
| Entropy changes accompanying association reactions of proteins | Q79644995 | ||
| P433 | issue | 6 | |
| P304 | page(s) | 1293-1301 | |
| P577 | publication date | 1997-06-01 | |
| P1433 | published in | Protein Science | Q7251445 |
| P1476 | title | On the calculation of binding free energies using continuum methods: application to MHC class I protein-peptide interactions | |
| P478 | volume | 6 |
| Q77365342 | A comparative study of ligand-receptor complex binding affinity prediction methods based on glycogen phosphorylase inhibitors |
| Q36082576 | Affinity and specificity of protein U1A-RNA complex formation based on an additive component free energy model |
| Q40169477 | Association entropy in adsorption processes. |
| Q27641254 | Binding Structures and Potencies of Oxidosqualene Cyclase Inhibitors with the Homologous Squalene−Hopene Cyclase |
| Q32124412 | Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase |
| Q35367681 | Binding sites in Escherichia coli dihydrofolate reductase communicate by modulating the conformational ensemble |
| Q34984697 | Calculating the free energy of association of transmembrane helices |
| Q25257719 | Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain |
| Q33631185 | Computational analysis of the binding specificity of Gleevec to Abl, c-Kit, Lck, and c-Src tyrosine kinases |
| Q47829750 | Computational approaches to molecular recognition. |
| Q58006839 | Computer Modeling of the Membrane Interaction of FYVE Domains |
| Q43947466 | Contributions to the binding free energy of ligands to avidin and streptavidin. |
| Q27639247 | Crystal structure of a non-canonical low-affinity peptide complexed with MHC class I: a new approach for vaccine design |
| Q73666443 | Customized versus universal scoring functions: application to class I MHC-peptide binding free energy predictions |
| Q49962243 | Direction-dependent force-induced dissociation dynamics of an entropic-driven lock-and-key assembly. |
| Q35596397 | Dynamics of Recognition between tRNA and elongation factor Tu |
| Q38272342 | Electrostatic contributions to protein-protein interactions: fast energetic filters for docking and their physical basis |
| Q34169304 | Electrostatic contributions to the binding free energy of the lambdacI repressor to DNA. |
| Q47959634 | Electrostatic effects in macromolecules: fundamental concepts and practical modeling |
| Q36737350 | Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids |
| Q73864357 | Empirical calculation of the relative free energies of peptide binding to the molecular chaperone DnaK |
| Q50637695 | Evaluation of electrostatic interactions. |
| Q35596415 | Exit strategies for charged tRNA from GluRS |
| Q34182722 | Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates |
| Q34186724 | Free diffusion of steroid hormones across biomembranes: a simplex search with implicit solvent model calculations |
| Q34176045 | Free energy decomposition of protein-protein interactions. |
| Q38329838 | Free energy determinants of binding the rRNA substrate and small ligands to ricin A-chain |
| Q34691182 | Free energy simulations come of age: protein-ligand recognition |
| Q51641693 | Free-energy component analysis of 40 protein-DNA complexes: a consensus view on the thermodynamics of binding at the molecular level. |
| Q51157769 | Generalized iterative annealing model for the action of RNA chaperones. |
| Q52079003 | Grafting of protein-protein interaction epitope. |
| Q24318965 | Identification and rational redesign of peptide ligands to CRIP1, a novel biomarker for cancers |
| Q33300586 | Identification of DNA-binding protein target sequences by physical effective energy functions: free energy analysis of lambda repressor-DNA complexes |
| Q28751619 | Integrated Modeling Program, Applied Chemical Theory (IMPACT) |
| Q31934059 | Knowledge-based structure prediction of MHC class I bound peptides: a study of 23 complexes |
| Q57136102 | Mean-field analysis of protein-protein interactions |
| Q27650387 | Metal-Mediated Self-Assembly of Protein Superstructures: Influence of Secondary Interactions on Protein Oligomerization and Aggregation |
| Q41679805 | Methodology for protein-ligand binding studies: application to a model for drug resistance, the HIV/FIV protease system |
| Q40280520 | Modeling electron transfer thermodynamics in protein complexes: interaction between two cytochromes c(3). |
| Q30476755 | Molecular dynamics of a protein surface: ion-residues interactions |
| Q40188101 | Molecular dynamics simulations show that conformational selection governs the binding preferences of imatinib for several tyrosine kinases |
| Q43909373 | Molecular modeling of class I and II alleles of the major histocompatibility complex in Salmo salar |
| Q36403929 | Natural HLA class I polymorphism controls the pathway of antigen presentation and susceptibility to viral evasion |
| Q44021056 | On the role of electrostatic interactions in the design of protein-protein interfaces |
| Q36640288 | Optimization of binding electrostatics: charge complementarity in the barnase-barstar protein complex. |
| Q74336775 | Predicting sequences and structures of MHC-binding peptides: a computational combinatorial approach |
| Q33682938 | Prediction of the binding energy for small molecules, peptides and proteins |
| Q73216554 | Prediction of the multimeric assembly of staphylococcal enterotoxin A with cell-surface protein receptors |
| Q34560652 | Protein surface dynamics: interaction with water and small solutes |
| Q24798732 | Proteomics in Vaccinology and Immunobiology: An Informatics Perspective of the Immunone |
| Q24304924 | RRM proteins interacting with the cap region of topoisomerase I |
| Q45964522 | Simulating electrostatic energies in proteins: perspectives and some recent studies of pKas, redox, and other crucial functional properties. |
| Q37948589 | Simulation of multihaem cytochromes |
| Q73090928 | Solvation energy and thermal stability of hydrophilization-modified alpha-chymotrypsin |
| Q46084222 | Solvation energy density occlusion approximation for evaluation of desolvation penalties in biomolecular interactions |
| Q35014298 | Structural basis of macromolecular recognition |
| Q42846855 | Structural determinants of trypsin affinity and specificity for cationic inhibitors |
| Q42001934 | Structure of human factor VIIa/tissue factor in complex with a peptide-mimetic inhibitor: high selectivity against thrombin by introducing two charged groups in P2 and P4. |
| Q34312495 | T-cell epitope prediction and immune complex simulation using molecular dynamics: state of the art and persisting challenges |
| Q36702419 | T-cell epitope vaccine design by immunoinformatics |
| Q33803629 | The AGBNP2 Implicit Solvation Model. |
| Q42155548 | The measured and calculated affinity of methyl- and methoxy-substituted benzoquinones for the Q(A) site of bacterial reaction centers |
| Q46853640 | Theory of biomolecular recognition |
| Q36943279 | Thermodynamic basis for promiscuity and selectivity in protein-protein interactions: PDZ domains, a case study |
| Q79169010 | Thrombin inhibitors with novel P1 binding pocket functionality: free energy of binding analysis |
| Q37621557 | Transition state and encounter complex for fast association of cytochrome c2 with bacterial reaction center |
| Q44080793 | Using DelPhi to compute electrostatic potentials and assess their contribution to interactions |
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