| Comparison of multiple Amber force fields and development of improved protein backbone parameters | 2006/09/15 | English | 5,456 |
| Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons | 1991/12/01 | English | 4,188 |
| Improved side‐chain torsion potentials for the Amber ff99SB protein force field | 2010/04/05 | English | 4,141 |
| Structure validation by Cα geometry: ϕ,ψ and Cβ deviation | 2003/01/08 | English | 3,583 |
| Essential dynamics of proteins | 1993/12/01 | English | 2,579 |
| The CCPN data model for NMR spectroscopy: Development of a software pipeline | 2005/04/06 | English | 2,487 |
| Improved protein–ligand docking using GOLD | 2003/08/01 | English | 2,084 |
| Funnels, pathways, and the energy landscape of protein folding: A synthesis | 1995/03/01 | English | 2,017 |
| Exploring protein native states and large‐scale conformational changes with a modified generalized born model | 2004/03/05 | English | 1,931 |
| Knowledge‐based protein secondary structure assignment | 1995/12/01 | English | 1,876 |
| A hierarchical approach to all‐atom protein loop prediction | 2004/03/05 | English | 1,639 |
| Very fast empirical prediction and rationalization of protein pKa values | 2005/11/17 | English | 1,632 |
| Structure and energetics of ligand binding to proteins: Escherichia coli dihydrofolate reductase‐trimethoprim, a drug‐receptor system | 1988/01/01 | English | 1,632 |
| Recognition of errors in three‐dimensional structures of proteins | 1993/12/01 | English | 1,543 |
| Primary structure effects on peptide group hydrogen exchange | 1993/09/01 | English | 1,425 |
| Prediction of protein cellular attributes using pseudo‐amino acid composition | 2001/03/07 | English | 1,301 |
| Scoring function for automated assessment of protein structure template quality | 2004/10/08 | English | 1,257 |
| Increasing the precision of comparative models with YASARA NOVA—a self‐parameterizing force field | 2002/03/27 | English | 1,145 |
| Prediction of protein subcellular localization | 2006/06/02 | English | 1,106 |
| Stereochemical quality of protein structure coordinates | 1992/04/01 | English | 1,092 |
| Database of homology‐derived protein structures and the structural meaning of sequence alignment | 1991/01/01 | English | 1,022 |
| The molten globule state as a clue for understanding the folding and cooperativity of globular‐protein structure | 1989/01/01 | English | 1,018 |
| ZDOCK: An initial‐stage protein‐docking algorithm | 2003/05/14 | English | 972 |
| Improving physical realism, stereochemistry, and side‐chain accuracy in homology modeling: Four approaches that performed well in CASP8 | 2009/01/01 | English | 963 |
| Combining evolutionary information and neural networks to predict protein secondary structure | 1994/05/01 | English | 959 |
| Improved prediction of protein side‐chain conformations with SCWRL4 | 2009/07/14 | English | 943 |
| Prediction of continuous B‐cell epitopes in an antigen using recurrent neural network | 2006/08/07 | English | 932 |
| Very fast prediction and rationalization of pKa values for protein–ligand complexes | 2008/05/22 | English | 869 |
| Evaluation of comparative protein modeling by MODELLER | 1995/11/01 | English | 849 |
| Automated docking of substrates to proteins by simulated annealing | 1990/01/01 | English | 754 |