A graph‐theory algorithm for rapid protein side‐chain prediction

The Protein Data Bank

2000 • 35,287 citations

Depth-First Search and Linear Graph Algorithms

1972 • 5,699 citations

PISCES: a protein sequence culling server

2003 • 1,699 citations

Enhanced genome annotation using structural profiles in the program 3D-PSSM 1 1Edited by J. Thornton

2000 • 1,494 citations

Tertiary templates for proteins

1987 • 1,485 citations

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation 1 1Edited by J. Thornton

1999 • 1,353 citations

The penultimate rotamer library

2000 • 1,024 citations

Backbone-dependent Rotamer Library for Proteins Application to Side-chain Prediction

1993 • 910 citations

Bayesian statistical analysis of protein side‐chain rotamer preferences

1997 • 792 citations

The dead-end elimination theorem and its use in protein side-chain positioning

1992 • 698 citations

Rotamer Libraries in the 21st Century

2002 • 639 citations

Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool

1997 • 565 citations

Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms 1 1Edited by J. Thornton

1999 • 523 citations

Analysis of the relationship between side-chain conformation and secondary structure in globular proteins

1987 • 422 citations

Extending the accuracy limits of prediction for side-chain conformations

2001 • 414 citations

Combinatorial algorithms: generation, enumeration, and search

2000 • 411 citations

A New Approach to the Rapid Determination of Protein Side Chain Conformations

1991 • 345 citations

Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains

1994 • 342 citations

Database algorithm for generating protein backbone and side-chain co-ordinates from a Cα trace

1991 • 324 citations

De novo design of the hydrophobic cores of proteins

1995 • 301 citations

Protein design automation

1996 • 291 citations

Efficient rotamer elimination applied to protein side-chains and related spin glasses

1994 • 279 citations

Prediction of protein side-chain conformation by packing optimization

1991 • 228 citations

Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics

2001 • 204 citations

Trading accuracy for speed: a quantitative comparison of search algorithms in protein sequence design 1 1Edited by J. Thornton

2000 • 190 citations

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

2000 • 167 citations

All in one: a highly detailed rotamer library improves both accuracy and speed in the modelling of sidechains by dead-end elimination

1997 • 146 citations

Side‐chain modeling with an optimized scoring function

2002 • 129 citations

Fast and accurate side‐chain topology and energy refinement (FASTER) as a new method for protein structure optimization

2002 • 119 citations

Branch-and-Terminate: a combinatorial optimization algorithm for protein design

1999 • 114 citations

Combinatorial algorithms

1999 • 105 citations

Enhanced dead-end elimination in the search for the global minimum energy conformation of a collection of protein side chains

1995 • 99 citations

A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modelling

1995 • 97 citations

Modeling Side-chain Conformation for Homologous Proteins Using an Energy-based Rotamer Search

1993 • 95 citations

Construction of side-chains in homology modelling

1989 • 93 citations

The fuzzy-end elimination theorem: correctly implementing the side chain placement algorithm based on the dead-end elimination theorem

1993 • 82 citations

Improved modeling of side-chains in proteins with rotamer-based methods: A flexible rotamer model

1999 • 81 citations

Comparative modeling of CASP3 targets using PSI‐BLAST and SCWRL

1999 • 64 citations

Side-chain prediction by neural networks and simulated annealing optimization

1995 • 61 citations

Prediction of Protein Side-chain Conformations from Local Three-dimensional Homology Relationships

1994 • 54 citations

Determinants of side chain conformational preferences in protein structures

1998 • 49 citations

The Dead-End Elimination Theorem: Mathematical Aspects, Implementation, Optimizations, Evaluation and Performance

2003 • 47 citations

Improvement of side-chain modeling in proteins with the self-consistent mean field theory method based on an analysis of the factors influencing prediction

1999 • 47 citations

Energy minimization method using automata network for sequence and side‐chain conformation prediction from given backbone geometry

1994 • 41 citations

Finding the global minimum: a fuzzy end elimination implementation

1995 • 29 citations

Incorporating knowledge-based biases into an energy-based side-chain modeling method: Application to comparative modeling of protein structure

2001 • 24 citations

Theoretical and algorithmical optimization of the dead-end elimination theorem.

1997 • 17 citations

Implicit solvation in the self-consistent mean field theory method: sidechain modelling and prediction of folding free energies of protein mutants.

2001 • 17 citations