| # | Title | Journal | Year | Citations |
|---|
| 1 | Comparison of multiple Amber force fields and development of improved protein backbone parameters | Proteins: Structure, Function and Bioinformatics | 2006 | 6,049 |
| 2 | Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons | Proteins: Structure, Function and Bioinformatics | 1991 | 5,360 |
| 3 | Improved side‐chain torsion potentials for the Amber ff99SB protein force field | Proteins: Structure, Function and Bioinformatics | 2010 | 4,694 |
| 4 | Structure validation by Cα geometry: ϕ,ψ and Cβ deviation | Proteins: Structure, Function and Bioinformatics | 2003 | 4,134 |
| 5 | Essential dynamics of proteins | Proteins: Structure, Function and Bioinformatics | 1993 | 2,927 |
| 6 | The CCPN data model for NMR spectroscopy: Development of a software pipeline | Proteins: Structure, Function and Bioinformatics | 2005 | 2,805 |
| 7 | Improved protein-ligand docking using GOLD | Proteins: Structure, Function and Bioinformatics | 2003 | 2,417 |
| 8 | Funnels, pathways, and the energy landscape of protein folding: A synthesis | Proteins: Structure, Function and Bioinformatics | 1995 | 2,415 |
| 9 | Knowledge-based protein secondary structure assignment | Proteins: Structure, Function and Bioinformatics | 1995 | 2,306 |
| 10 | Exploring protein native states and large-scale conformational changes with a modified generalized born model | Proteins: Structure, Function and Bioinformatics | 2004 | 2,068 |
| 11 | Why are ?natively unfolded? proteins unstructured under physiologic conditions? | Proteins: Structure, Function and Bioinformatics | 2000 | 1,931 |
| 12 | Recognition of errors in three-dimensional structures of proteins | Proteins: Structure, Function and Bioinformatics | 1993 | 1,913 |
| 13 | A hierarchical approach to all-atom protein loop prediction | Proteins: Structure, Function and Bioinformatics | 2004 | 1,874 |
| 14 | Structure and energetics of ligand binding to proteins:Escherichia coli dihydrofolate reductase-trimethoprim, a drug-receptor system | Proteins: Structure, Function and Bioinformatics | 1988 | 1,848 |
| 15 | Primary structure effects on peptide group hydrogen exchange | Proteins: Structure, Function and Bioinformatics | 1993 | 1,805 |
| 16 | Very fast empirical prediction and rationalization of protein pKa values | Proteins: Structure, Function and Bioinformatics | 2005 | 1,771 |
| 17 | Prediction of protein cellular attributes using pseudo-amino acid composition | Proteins: Structure, Function and Bioinformatics | 2001 | 1,729 |
| 18 | Scoring function for automated assessment of protein structure template quality | Proteins: Structure, Function and Bioinformatics | 2004 | 1,697 |
| 19 | Database of homology-derived protein structures and the structural meaning of sequence alignment | Proteins: Structure, Function and Bioinformatics | 1991 | 1,600 |
| 20 | Sequence complexity of disordered protein | Proteins: Structure, Function and Bioinformatics | 2001 | 1,547 |
| 21 | Combining evolutionary information and neural networks to predict protein secondary structure | Proteins: Structure, Function and Bioinformatics | 1994 | 1,465 |
| 22 | Stereochemical quality of protein structure coordinates | Proteins: Structure, Function and Bioinformatics | 1992 | 1,436 |
| 23 | The molten globule state as a clue for understanding the folding and cooperativity of globular-protein structure | Proteins: Structure, Function and Bioinformatics | 1989 | 1,412 |
| 24 | Prediction of protein subcellular localization | Proteins: Structure, Function and Bioinformatics | 2006 | 1,314 |
| 25 | Increasing the precision of comparative models with YASARA NOVA-a self-parameterizing force field | Proteins: Structure, Function and Bioinformatics | 2002 | 1,277 |
| 26 | ZDOCK: An initial-stage protein-docking algorithm | Proteins: Structure, Function and Bioinformatics | 2003 | 1,220 |
| 27 | Improved prediction of protein side‐chain conformations with SCWRL4 | Proteins: Structure, Function and Bioinformatics | 2009 | 1,161 |
| 28 | Prediction of continuous B-cell epitopes in an antigen using recurrent neural network | Proteins: Structure, Function and Bioinformatics | 2006 | 1,146 |
| 29 | Principles of docking: An overview of search algorithms and a guide to scoring functions | Proteins: Structure, Function and Bioinformatics | 2002 | 1,130 |
| 30 | Automated docking of substrates to proteins by simulated annealing | Proteins: Structure, Function and Bioinformatics | 1990 | 1,109 |
| 31 | Improving physical realism, stereochemistry, and side‐chain accuracy in homology modeling: Four approaches that performed well in CASP8 | Proteins: Structure, Function and Bioinformatics | 2009 | 1,105 |
| 32 | Evaluation of comparative protein modeling by MODELLER | Proteins: Structure, Function and Bioinformatics | 1995 | 1,035 |
| 33 | A workbench for multiple alignment construction and analysis | Proteins: Structure, Function and Bioinformatics | 1991 | 1,012 |
| 34 | The penultimate rotamer library | Proteins: Structure, Function and Bioinformatics | 2000 | 977 |
| 35 | Very fast prediction and rationalization of pKa values for protein–ligand complexes | Proteins: Structure, Function and Bioinformatics | 2008 | 938 |
| 36 | QMEAN: A comprehensive scoring function for model quality assessment | Proteins: Structure, Function and Bioinformatics | 2008 | 888 |
| 37 | Protein secondary structure and circular dichroism: A practical guide | Proteins: Structure, Function and Bioinformatics | 1990 | 886 |
| 38 | What are the dielectric ?constants? of proteins and how to validate electrostatic models? | Proteins: Structure, Function and Bioinformatics | 2001 | 865 |
| 39 | Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations | Proteins: Structure, Function and Bioinformatics | 1991 | 821 |
| 40 | Correlated mutations and residue contacts in proteins | Proteins: Structure, Function and Bioinformatics | 1994 | 801 |
| 41 | Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis | Proteins: Structure, Function and Bioinformatics | 1988 | 794 |
| 42 | Prediction of protein stability changes for single-site mutations using support vector machines | Proteins: Structure, Function and Bioinformatics | 2005 | 784 |
| 43 | Is allostery an intrinsic property of all dynamic proteins? | Proteins: Structure, Function and Bioinformatics | 2004 | 779 |
| 44 | The VSGB 2.0 model: A next generation energy model for high resolution protein structure modeling | Proteins: Structure, Function and Bioinformatics | 2011 | 773 |
| 45 | Making optimal use of empirical energy functions: Force-field parameterization in crystal space | Proteins: Structure, Function and Bioinformatics | 2004 | 772 |
| 46 | Protein-ligand docking: Current status and future challenges | Proteins: Structure, Function and Bioinformatics | 2006 | 761 |
| 47 | Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme | Proteins: Structure, Function and Bioinformatics | 1998 | 746 |
| 48 | Ab initio protein structure assembly using continuous structure fragments and optimized knowledge‐based force field | Proteins: Structure, Function and Bioinformatics | 2012 | 744 |
| 49 | α-Helical coiled coils and bundles: How to design an α-helical protein | Proteins: Structure, Function and Bioinformatics | 1990 | 732 |
| 50 | Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: Effects of ionic strength and amino-acid modification | Proteins: Structure, Function and Bioinformatics | 1986 | 730 |
