| # | Title | Journal | Year | Citations |
|---|
|
| 1 | Comparison of multiple Amber force fields and development of improved protein backbone parameters | Proteins: Structure, Function and Bioinformatics | 2006 | 6,202 |
| 2 | Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons | Proteins: Structure, Function and Bioinformatics | 1991 | 5,370 |
| 3 | Improved side‐chain torsion potentials for the Amber ff99SB protein force field | Proteins: Structure, Function and Bioinformatics | 2010 | 4,925 |
| 4 | Structure validation by Cα geometry: ϕ,ψ and Cβ deviation | Proteins: Structure, Function and Bioinformatics | 2003 | 4,212 |
| 5 | Essential dynamics of proteins | Proteins: Structure, Function and Bioinformatics | 1993 | 3,004 |
| 6 | The CCPN data model for NMR spectroscopy: Development of a software pipeline | Proteins: Structure, Function and Bioinformatics | 2005 | 2,900 |
| 7 | Improved protein-ligand docking using GOLD | Proteins: Structure, Function and Bioinformatics | 2003 | 2,491 |
| 8 | Funnels, pathways, and the energy landscape of protein folding: A synthesis | Proteins: Structure, Function and Bioinformatics | 1995 | 2,444 |
| 9 | Knowledge-based protein secondary structure assignment | Proteins: Structure, Function and Bioinformatics | 1995 | 2,339 |
| 10 | Exploring protein native states and large-scale conformational changes with a modified generalized born model | Proteins: Structure, Function and Bioinformatics | 2004 | 2,126 |
| 11 | A hierarchical approach to all-atom protein loop prediction | Proteins: Structure, Function and Bioinformatics | 2004 | 1,980 |
| 12 | Why are ?natively unfolded? proteins unstructured under physiologic conditions? | Proteins: Structure, Function and Bioinformatics | 2000 | 1,964 |
| 13 | Recognition of errors in three‐dimensional structures of proteins | Proteins: Structure, Function and Bioinformatics | 1993 | 1,950 |
| 14 | Structure and energetics of ligand binding to proteins:Escherichia coli dihydrofolate reductase-trimethoprim, a drug-receptor system | Proteins: Structure, Function and Bioinformatics | 1988 | 1,881 |
| 15 | Primary structure effects on peptide group hydrogen exchange | Proteins: Structure, Function and Bioinformatics | 1993 | 1,820 |
| 16 | Very fast empirical prediction and rationalization of protein pKa values | Proteins: Structure, Function and Bioinformatics | 2005 | 1,808 |
| 17 | Scoring function for automated assessment of protein structure template quality | Proteins: Structure, Function and Bioinformatics | 2004 | 1,785 |
| 18 | Prediction of protein cellular attributes using pseudo-amino acid composition | Proteins: Structure, Function and Bioinformatics | 2001 | 1,764 |
| 19 | Database of homology-derived protein structures and the structural meaning of sequence alignment | Proteins: Structure, Function and Bioinformatics | 1991 | 1,608 |
| 20 | Sequence complexity of disordered protein | Proteins: Structure, Function and Bioinformatics | 2001 | 1,576 |
| 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 | 1,453 |
| 23 | The molten globule state as a clue for understanding the folding and cooperativity of globular-protein structure | Proteins: Structure, Function and Bioinformatics | 1989 | 1,420 |
| 24 | Prediction of protein subcellular localization | Proteins: Structure, Function and Bioinformatics | 2006 | 1,386 |
| 25 | Increasing the precision of comparative models with YASARA NOVA-a self-parameterizing force field | Proteins: Structure, Function and Bioinformatics | 2002 | 1,304 |
| 26 | ZDOCK: An initial-stage protein-docking algorithm | Proteins: Structure, Function and Bioinformatics | 2003 | 1,249 |
| 27 | Prediction of continuous B-cell epitopes in an antigen using recurrent neural network | Proteins: Structure, Function and Bioinformatics | 2006 | 1,217 |
| 28 | Improved prediction of protein side‐chain conformations with SCWRL4 | Proteins: Structure, Function and Bioinformatics | 2009 | 1,187 |
| 29 | Improving physical realism, stereochemistry, and side‐chain accuracy in homology modeling: Four approaches that performed well in CASP8 | Proteins: Structure, Function and Bioinformatics | 2009 | 1,167 |
| 30 | Effective energy function for proteins in solution | Proteins: Structure, Function and Bioinformatics | 1999 | 1,153 |
| 31 | Principles of docking: An overview of search algorithms and a guide to scoring functions | Proteins: Structure, Function and Bioinformatics | 2002 | 1,147 |
| 32 | Automated docking of substrates to proteins by simulated annealing | Proteins: Structure, Function and Bioinformatics | 1990 | 1,130 |
| 33 | Pfam: A comprehensive database of protein domain families based on seed alignments | Proteins: Structure, Function and Bioinformatics | 1997 | 1,051 |
| 34 | Evaluation of comparative protein modeling by MODELLER | Proteins: Structure, Function and Bioinformatics | 1995 | 1,041 |
| 35 | A workbench for multiple alignment construction and analysis | Proteins: Structure, Function and Bioinformatics | 1991 | 1,012 |
| 36 | The penultimate rotamer library | Proteins: Structure, Function and Bioinformatics | 2000 | 990 |
| 37 | Very fast prediction and rationalization of pKa values for protein–ligand complexes | Proteins: Structure, Function and Bioinformatics | 2008 | 967 |
| 38 | QMEAN: A comprehensive scoring function for model quality assessment | Proteins: Structure, Function and Bioinformatics | 2008 | 909 |
| 39 | Protein secondary structure and circular dichroism: A practical guide | Proteins: Structure, Function and Bioinformatics | 1990 | 895 |
| 40 | What are the dielectric ?constants? of proteins and how to validate electrostatic models? | Proteins: Structure, Function and Bioinformatics | 2001 | 870 |
| 41 | Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations | Proteins: Structure, Function and Bioinformatics | 1991 | 859 |
| 42 | Prediction of protein stability changes for single‐site mutations using support vector machines | Proteins: Structure, Function and Bioinformatics | 2006 | 842 |
| 43 | The VSGB 2.0 model: A next generation energy model for high resolution protein structure modeling | Proteins: Structure, Function and Bioinformatics | 2011 | 838 |
| 44 | Correlated mutations and residue contacts in proteins | Proteins: Structure, Function and Bioinformatics | 1994 | 810 |
| 45 | Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis | Proteins: Structure, Function and Bioinformatics | 1988 | 803 |
| 46 | Is allostery an intrinsic property of all dynamic proteins? | Proteins: Structure, Function and Bioinformatics | 2004 | 793 |
| 47 | Protein-ligand docking: Current status and future challenges | Proteins: Structure, Function and Bioinformatics | 2006 | 790 |
| 48 | Making optimal use of empirical energy functions: Force-field parameterization in crystal space | Proteins: Structure, Function and Bioinformatics | 2004 | 788 |
| 49 | Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking | Proteins: Structure, Function and Bioinformatics | 1999 | 780 |
| 50 | Ab initio protein structure assembly using continuous structure fragments and optimized knowledge‐based force field | Proteins: Structure, Function and Bioinformatics | 2012 | 776 |
