| # | Title | Journal | Year | Citations |
|---|
| 1 | Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites | Protein Engineering, Design and Selection | 1997 | 5,051 |
| 2 | LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions | Protein Engineering, Design and Selection | 1995 | 4,648 |
| 3 | The α/β hydrolase fold | Protein Engineering, Design and Selection | 1992 | 1,887 |
| 4 | Protein structure alignment by incremental combinatorial extension (CE) of the optimal path | Protein Engineering, Design and Selection | 1998 | 1,760 |
| 5 | Crystal structure of human serum albumin at 2.5 Å resolution | Protein Engineering, Design and Selection | 1999 | 1,533 |
| 6 | Twilight zone of protein sequence alignments | Protein Engineering, Design and Selection | 1999 | 1,446 |
| 7 | ALSCRIPT: a tool to format multiple sequence alignments | Protein Engineering, Design and Selection | 1993 | 1,104 |
| 8 | Feature-based prediction of non-classical and leaderless protein secretion | Protein Engineering, Design and Selection | 2004 | 1,089 |
| 9 | A new method for predicting binding affinity in computer-aided drug design | Protein Engineering, Design and Selection | 1994 | 1,064 |
| 10 | Quantitative analysis of protein far UV circular dichroism spectra by neural networks | Protein Engineering, Design and Selection | 1992 | 997 |
| 11 | Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence | Protein Engineering, Design and Selection | 1990 | 938 |
| 12 | Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method | Protein Engineering, Design and Selection | 1997 | 930 |
| 13 | Evaluation of secondary structure of proteins from UV circular dichroism spectra using an unsupervised learning neural network | Protein Engineering, Design and Selection | 1993 | 916 |
| 14 | Single-stranded DNA ‘blue’ T7 promoter plasmids: a versatile tandem promoter system for cloning and protein engineering | Protein Engineering, Design and Selection | 1986 | 848 |
| 15 | Factors enhancing protein thermostability | Protein Engineering, Design and Selection | 2000 | 807 |
| 16 | Conformational change of proteins arising from normal mode calculations | Protein Engineering, Design and Selection | 2001 | 796 |
| 17 | Tobacco etch virus protease: mechanism of autolysis and rational design of stable mutants with wild-type catalytic proficiency | Protein Engineering, Design and Selection | 2001 | 729 |
| 18 | Analysis and prediction of leucine-rich nuclear export signals | Protein Engineering, Design and Selection | 2004 | 721 |
| 19 | Sequence differences between glycosylated and non-glycosylated Asn-X-Thr/Ser acceptor sites: implications for protein engineering | Protein Engineering, Design and Selection | 1990 | 674 |
| 20 | A synthetic IgG-binding domain based on staphylococcal protein A | Protein Engineering, Design and Selection | 1987 | 662 |
| 21 | An attempt to unify the structure of polymerases | Protein Engineering, Design and Selection | 1990 | 616 |
| 22 | ‘Knobs-into-holes’ engineering of antibody CH3 domains for heavy chain heterodimerization | Protein Engineering, Design and Selection | 1996 | 616 |
| 23 | Machine learning approaches for the prediction of signal peptides and other protein sorting signals | Protein Engineering, Design and Selection | 1999 | 546 |
| 24 | Design of the linkers which effectively separate domains of a bifunctional fusion protein | Protein Engineering, Design and Selection | 2001 | 535 |
| 25 | Folding funnels and binding mechanisms | Protein Engineering, Design and Selection | 1999 | 534 |
| 26 | Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of -amylase-related proteins | Protein Engineering, Design and Selection | 2006 | 530 |
| 27 | Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints. Application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2 | Protein Engineering, Design and Selection | 1988 | 513 |
| 28 | CSS-Palm 2.0: an updated software for palmitoylation sites prediction | Protein Engineering, Design and Selection | 2008 | 511 |
| 29 | Prediction of proprotein convertase cleavage sites | Protein Engineering, Design and Selection | 2004 | 499 |
| 30 | Attenuation of green fluorescent protein half-life in mammalian cells | Protein Engineering, Design and Selection | 1999 | 467 |
| 31 | An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies | Protein Engineering, Design and Selection | 1996 | 426 |
| 32 | Similarity of phylogenetic trees as indicator of protein–protein interaction | Protein Engineering, Design and Selection | 2001 | 425 |
| 33 | Sequence and structure of VH domain from naturally occurring camel heavy chain immunoglobulins lacking light chains | Protein Engineering, Design and Selection | 1994 | 407 |
| 34 | Hydrogen bonds and salt bridges across protein-protein interfaces | Protein Engineering, Design and Selection | 1997 | 385 |
| 35 | β-Turns and their distortions: a proposed new nomenclature | Protein Engineering, Design and Selection | 1990 | 380 |
| 36 | Consensus guided mutagenesis of Renilla luciferase yields enhanced stability and light output | Protein Engineering, Design and Selection | 2006 | 371 |
| 37 | Knowledge based modelling of homologous proteins, part I: three-dimensional frameworks derived from the simultaneous superposition of multiple structures | Protein Engineering, Design and Selection | 1987 | 365 |
| 38 | Incorporation of non-local interactions in protein secondary structure prediction from the amino acid sequence | Protein Engineering, Design and Selection | 1996 | 337 |
| 39 | An improved yeast transformation method for the generation of very large human antibody libraries | Protein Engineering, Design and Selection | 2010 | 337 |
| 40 | Protein subcellular location prediction | Protein Engineering, Design and Selection | 1999 | 334 |
| 41 | The function of tryptophan residues in membrane proteins | Protein Engineering, Design and Selection | 1992 | 332 |
| 42 | Homology modelling and protein engineering strategy of subtilases, the family of subtilisin-like serine proteinases | Protein Engineering, Design and Selection | 1991 | 331 |
| 43 | An analysis of protein domain linkers: their classification and role in protein folding | Protein Engineering, Design and Selection | 2002 | 330 |
| 44 | Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details | Protein Engineering, Design and Selection | 2009 | 325 |
| 45 | Convex constraint analysis: a natural deconvolution of circular dichroism curves of proteins | Protein Engineering, Design and Selection | 1991 | 317 |
| 46 | Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins | Protein Engineering, Design and Selection | 1996 | 317 |
| 47 | An algorithm for protein secondary structure prediction based on class prediction | Protein Engineering, Design and Selection | 1987 | 316 |
| 48 | The price of lost freedom: entropy of bimolecular complex formation | Protein Engineering, Design and Selection | 1989 | 312 |
| 49 | Cleavage-site motifs in mitochondrial targeting peptides | Protein Engineering, Design and Selection | 1990 | 311 |
| 50 | SOPM: a self-optimized method for protein secondary structure prediction | Protein Engineering, Design and Selection | 1994 | 296 |
