Predicting Binding Affinities of Protein Ligands from Three-Dimensional Models: Application to Peptide Binding to Class I Major Histocompatibility Proteins

van der Waals Volumes and Radii

1964 • 18,329 citations

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

1995 • 12,826 citations

The protein data bank: A computer-based archival file for macromolecular structures

1977 • 8,627 citations

Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins

1988 • 3,852 citations

Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules

1991 • 2,447 citations

Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes.

1997 • 1,617 citations

Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains.

1994 • 1,400 citations

An αβ T Cell Receptor Structure at 2.5 Å and Its Orientation in the TCR-MHC Complex

1996 • 1,282 citations

A new method for predicting binding affinity in computer-aided drug design

1994 • 1,154 citations

Calculating the electrostatic potential of molecules in solution: Method and error assessment

1988 • 1,096 citations

Refined structure of the human histocompatibility antigen HLA-A2 at 2.6 Å resolution

1991 • 1,079 citations

Association of class I major histocompatibility heavy and light chains induced by viral peptides

1989 • 995 citations

The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure

1994 • 975 citations

Calculation of the electric potential in the active site cleft due to α-helix dipoles

1982 • 931 citations

Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis

1988 • 829 citations

Focusing of electric fields in the active site of Cu‐Zn superoxide dismutase: Effects of ionic strength and amino‐acid modification

1986 • 759 citations

Structural Basis of Plasticity in T Cell Receptor Recognition of a Self Peptide-MHC Antigen

1998 • 685 citations

The antigenic identity of peptide-MHC complexes: A comparison of the conformations of five viral peptides presented by HLA-A2

1993 • 681 citations

The three-dimensional structure of HLA-B27 at 2.1 Å resolution suggests a general mechanism for tight peptide binding to MHC

1992 • 670 citations

Prominent role of secondary anchor residues in peptide binding to HLA-A2.1 molecules

1993 • 630 citations

Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs.

1998 • 425 citations

Molecular docking using shape descriptors

1992 • 420 citations

Different length peptides bind to HLA-Aw68 similarly at their ends but bulge out in the middle

1992 • 414 citations

PLS: Partial Least Squares Projections to Latent Structures

1993 • 375 citations

Importance of Peptide Amino and Carboxyl Termini to the Stability of MHC Class I Molecules

1994 • 294 citations

The Structure of the Upper Atmosphere of Mars: In Situ Accelerometer Measurements from Mars Global Surveyor

1998 • 271 citations

Two complementary methods for predicting peptides binding major histocompatibility complex molecules

1997 • 261 citations

Advances and Continuing Challenges in Achieving Realistic and Predictive Simulations of the Properties of Organic and Biological Molecules

1996 • 258 citations

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.

1995 • 254 citations

VALIDATE: A New Method for the Receptor-Based Prediction of Binding Affinities of Novel Ligands

1996 • 233 citations

Peptide binding to the most frequent HLA-A class I alleles measured by quantitative molecular binding assays

1994 • 233 citations

Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches

1993 • 227 citations

A priori prediction of activity for HIV-1 protease inhibitors employing energy minimization in the active site

1995 • 224 citations

On the calculation of binding free energies using continuum methods: Application to MHC class I protein‐peptide interactions

1997 • 191 citations

Neural network-based prediction of candidate T-cell epitopes

1998 • 180 citations

HLA Class I nucleotide sequences, 1995

1995 • 138 citations

What determines the strength of noncovalent association of ligands to proteins in aqueous solution?

1993 • 136 citations

Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model.

1998 • 133 citations

An empirical examination of potential-energy minimization using the well-determined structure of the protein crambin

1986 • 102 citations

Affinity and Specificity of Serine Endopeptidase-Protein Inhibitor Interactions

1993 • 100 citations

Molecular Dynamics Simulation of MHC-Peptide Complexes as a Tool for Predicting Potential T Cell Epitopes

1994 • 100 citations

Ranking potential binding peptides to MHC molecules by a computational threading approach

1995 • 100 citations

Peptide binding specificity of major histocompatibility complex class I resolved into an array of apparently independent subspecificities: quantitation by peptide libraries and improved prediction of binding

1996 • 99 citations

Differences in MHC class I self peptide repertoires among HLA-A2 subtypes.

1995 • 97 citations

Computational Alchemy To Calculate Absolute Protein−Ligand Binding Free Energy

1998 • 93 citations

Pseudoreceptor Modeling: The Construction of Three-Dimensional Receptor Surrogates

1995 • 91 citations

Fibrous Mini-Collagens in Hydra Nematocysts

1994 • 86 citations

Monte Carlo docking of oligopeptides to proteins

1992 • 86 citations

A Structure-Based Algorithm to Predict Potential Binding Peptides to MHC Molecules with Hydrophobic Binding Pockets

1997 • 77 citations

Competitive assessment of protein fold recognition and alignment accuracy

1997 • 76 citations

Description and prediction of peptide-MHC binding: the ‘human MHC project’

1999 • 70 citations

Peptide binding by class I and class II MHC molecules

1997 • 70 citations

Computing the Structure of Bound Peptides

1993 • 65 citations

Consistency in structural energetics of protein folding and peptide recognition

1997 • 49 citations

Free energy mapping of class I MHC molecules and structural determination of bound peptides

1996 • 49 citations

The structures and energetics of fluorine-substituted phosphonium ylides

1986 • 49 citations

Knowledge-based structure prediction of MHC class I bound peptides: a study of 23 complexes

1998 • 48 citations

Molecular dynamics study of a complex between the human histocompatibility antigen HLA‐A2 and the IMP58‐66 nonapeptide from influenza virus matrix protein

1992 • 48 citations

Shared fine specificity between T-cell receptors and an antibody recognizing a peptide/major histocompatibility class I complex.

1996 • 47 citations

A structural and energetics analysis of the binding of a series of N-acetylneuraminic-acid-based inhibitors to influenza virus sialidase

1996 • 38 citations

Computational method for relative binding energies of enzyme‐substrate complexes

1996 • 34 citations

Designing an Optimum Guest for a Host Using Multimolecule Free Energy Calculations: Predicting the Best Ligand for Rebek's “Tennis Ball”

1998 • 31 citations

Statistical evidence for a galactic origin of gamma-ray bursts

1991 • 30 citations

Toward computational determination of peptide‐receptor structure

1993 • 25 citations

Calculation of binding energy differences for receptor–ligand systems using the Poisson‐Boltzmann method

1995 • 25 citations

Peptide docking using dynamic programming

1996 • 23 citations

Toward a predictive understanding of molecular recognition

1998 • 15 citations

Recent advances in structure-based ligand design using molecular dynamics and Monte Carlo methods.

1998 • 6 citations