Solvation energy in protein folding and binding.

CHARMM: the biomolecular simulation program. J Comput Chem (2009) 27.71

Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci (1993) 7.90

The statistical-thermodynamic basis for computation of binding affinities: a critical review. Biophys J (1997) 7.64

Desiccation tolerance of prokaryotes. Microbiol Rev (1994) 5.70

3D domain swapping: a mechanism for oligomer assembly. Protein Sci (1995) 4.96

Domain swapping: entangling alliances between proteins. Proc Natl Acad Sci U S A (1994) 4.20

A functionally defined model for the M2 proton channel of influenza A virus suggests a mechanism for its ion selectivity. Proc Natl Acad Sci U S A (1997) 4.03

VADAR: a web server for quantitative evaluation of protein structure quality. Nucleic Acids Res (2003) 3.95

Do salt bridges stabilize proteins? A continuum electrostatic analysis. Protein Sci (1994) 3.92

Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. Proc Natl Acad Sci U S A (1987) 3.68

An information theory model of hydrophobic interactions. Proc Natl Acad Sci U S A (1996) 3.40

Atomic solvation parameters applied to molecular dynamics of proteins in solution. Protein Sci (1992) 3.05

Calculation of the free energy of association for protein complexes. Protein Sci (1992) 3.03

Statistical potentials for fold assessment. Protein Sci (2002) 2.92

Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials. Biophys J (2006) 2.88

Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures. Proc Natl Acad Sci U S A (1999) 2.86

Protein design automation. Protein Sci (1996) 2.69

Where metal ions bind in proteins. Proc Natl Acad Sci U S A (1990) 2.56

Drying-induced hydrophobic polymer collapse. Proc Natl Acad Sci U S A (2002) 2.56

Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms. Proc Natl Acad Sci U S A (2006) 2.56

An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields. Proteins (2009) 2.44

The histone fold: a ubiquitous architectural motif utilized in DNA compaction and protein dimerization. Proc Natl Acad Sci U S A (1995) 2.40

A molecular mechanism for osmolyte-induced protein stability. Proc Natl Acad Sci U S A (2006) 2.36

Virus Particle Explorer (VIPER), a website for virus capsid structures and their computational analyses. J Virol (2001) 2.34

Simulation of the folding equilibrium of alpha-helical peptides: a comparison of the generalized Born approximation with explicit solvent. Proc Natl Acad Sci U S A (2003) 2.31

Mutagenesis of the putative fusion domain of the Semliki Forest virus spike protein. J Virol (1991) 2.30

Transmembrane helix predictions revisited. Protein Sci (2002) 2.28

Automated design of the surface positions of protein helices. Protein Sci (1997) 2.26

Folding simulations of a three-stranded antiparallel beta -sheet peptide. Proc Natl Acad Sci U S A (2000) 2.18

Perfection of a synaptic receptor: kinetics and energetics of the acetylcholine receptor. Proc Natl Acad Sci U S A (1989) 2.13

X-ray crystal structures of the oxidized and reduced forms of the rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus. Protein Sci (1992) 2.11

Kinetics of desolvation-mediated protein-protein binding. Biophys J (2000) 2.03

Structural basis for light-dependent signaling in the dimeric LOV domain of the photosensor YtvA. J Mol Biol (2007) 1.90

Structural analysis based on state-space modeling. Protein Sci (1993) 1.89

Refined structure of dimeric diphtheria toxin at 2.0 A resolution. Protein Sci (1994) 1.88

Identification of a second aryl phosphate-binding site in protein-tyrosine phosphatase 1B: a paradigm for inhibitor design. Proc Natl Acad Sci U S A (1997) 1.87

Structure of the reaction center from Rhodobacter sphaeroides R-26: membrane-protein interactions. Proc Natl Acad Sci U S A (1987) 1.84

Hydrophobicity regained. Protein Sci (1997) 1.80

Positioning of proteins in membranes: a computational approach. Protein Sci (2006) 1.79

A simple physical model for scaling in protein-protein interaction networks. Proc Natl Acad Sci U S A (2005) 1.78

Free energy determinants of tertiary structure and the evaluation of protein models. Protein Sci (2000) 1.71

Refined structure of monomeric diphtheria toxin at 2.3 A resolution. Protein Sci (1994) 1.64

Discrimination of native protein structures using atom-atom contact scoring. Proc Natl Acad Sci U S A (2003) 1.56

Quantification of the hydrophobic interaction by simulations of the aggregation of small hydrophobic solutes in water. Proc Natl Acad Sci U S A (2001) 1.55

Long time dynamics of Met-enkephalin: comparison of explicit and implicit solvent models. Biophys J (2002) 1.52

Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size. Mol Syst Biol (2008) 1.50

The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation. Proc Natl Acad Sci U S A (1998) 1.49

The crystal structure of a mutant protein with altered but improved hydrophobic core packing. Proc Natl Acad Sci U S A (1994) 1.48

A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations. PLoS Comput Biol (2009) 1.46

Determination of intrinsic hydrophilicity/hydrophobicity of amino acid side chains in peptides in the absence of nearest-neighbor or conformational effects. Biopolymers (2006) 1.46

Dependence of conformational stability on hydrophobicity of the amino acid residue in a series of variant proteins substituted at a unique position of tryptophan synthase alpha subunit. Proc Natl Acad Sci U S A (1987) 1.46

The role of position a in determining the stability and oligomerization state of alpha-helical coiled coils: 20 amino acid stability coefficients in the hydrophobic core of proteins. Protein Sci (1999) 1.45

Free energy of burying hydrophobic residues in the interface between protein subunits. Proc Natl Acad Sci U S A (1998) 1.45

The AGBNP2 Implicit Solvation Model. J Chem Theory Comput (2009) 1.43

Electrostatic interactions in the GCN4 leucine zipper: substantial contributions arise from intramolecular interactions enhanced on binding. Protein Sci (1999) 1.42

Optimal sequence selection in proteins of known structure by simulated evolution. Proc Natl Acad Sci U S A (1994) 1.41

Biomolecular electrostatics and solvation: a computational perspective. Q Rev Biophys (2012) 1.39

Thoroughly sampling sequence space: large-scale protein design of structural ensembles. Protein Sci (2002) 1.39

Protein model structure evaluation using the solvation free energy of folding. Proc Natl Acad Sci U S A (1990) 1.38

Architecture of helix bundle membrane proteins: an analysis of cytochrome c oxidase from bovine mitochondria. Protein Sci (1997) 1.38

Prediction of charge-induced molecular alignment of biomolecules dissolved in dilute liquid-crystalline phases. Biophys J (2004) 1.38

A test on peptide stability of AMBER force fields with implicit solvation. J Phys Chem B (2008) 1.38

Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics. Biophys J (2008) 1.36

Direct measurement of salt-bridge solvation energies using a peptide model system: implications for protein stability. Proc Natl Acad Sci U S A (1996) 1.35

Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch. Chem Biol (2008) 1.35

Prediction of protein complexes using empirical free energy functions. Protein Sci (1996) 1.33

Comparison of atomic solvation parametric sets: applicability and limitations in protein folding and binding. Protein Sci (1995) 1.33

The central proline of an internal viral fusion peptide serves two important roles. J Virol (2000) 1.33

Local water bridges and protein conformational stability. Protein Sci (1999) 1.32

Bacterial HA1 vaccine against pandemic H5N1 influenza virus: evidence of oligomerization, hemagglutination, and cross-protective immunity in ferrets. J Virol (2010) 1.31

Excluded volume approximation to protein-solvent interaction. The solvent contact model. Biophys J (1990) 1.30

Computational methods for biomolecular electrostatics. Methods Cell Biol (2008) 1.27

A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys. Nucleic Acids Res (2004) 1.27

The protein-folding problem: the native fold determines packing, but does packing determine the native fold? Proc Natl Acad Sci U S A (1991) 1.26

Giant protein kinases: domain interactions and structural basis of autoregulation. EMBO J (1996) 1.24

SIMS: computation of a smooth invariant molecular surface. Biophys J (1997) 1.24

Interconvertible lac repressor-DNA loops revealed by single-molecule experiments. PLoS Biol (2008) 1.23

Protocol for MM/PBSA molecular dynamics simulations of proteins. Biophys J (2003) 1.22

A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design. Protein Sci (1995) 1.21

The C-terminal domain of yeast PCNA is required for physical and functional interactions with Cdc9 DNA ligase. Nucleic Acids Res (2007) 1.21

Prediction of amino acid sequence from structure. Protein Sci (2000) 1.19

A streptavidin mutant with altered ligand-binding specificity. Proc Natl Acad Sci U S A (1998) 1.18

The "macromolecular tourist": universal temperature dependence of thermal diffusion in aqueous colloidal suspensions. Eur Phys J E Soft Matter (2006) 1.17

A combined computational and functional approach identifies new residues involved in pH-dependent gating of ASIC1a. J Biol Chem (2010) 1.17

Energy functions for protein design I: efficient and accurate continuum electrostatics and solvation. Protein Sci (2004) 1.17

YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops. RNA (2012) 1.16

Discriminating compact nonnative structures from the native structure of globular proteins. Proc Natl Acad Sci U S A (1995) 1.15

Are protein folds atypical? Proc Natl Acad Sci U S A (1998) 1.15

An intersubunit hydrogen bond in the nicotinic acetylcholine receptor that contributes to channel gating. J Biol Chem (2008) 1.14

Mapping the surface properties of macromolecules. Protein Sci (1993) 1.14

Hydrophobic hydration of amphipathic peptides. Biophys J (1999) 1.14

Structure-based conformational preferences of amino acids. Proc Natl Acad Sci U S A (1999) 1.13

Sequence signatures of direct complementarity between mRNAs and cognate proteins on multiple levels. Nucleic Acids Res (2012) 1.12

A solvent model for simulations of peptides in bilayers. I. Membrane-promoting alpha-helix formation. Biophys J (1999) 1.12

The weighted-volume derivative of a space-filling diagram. Proc Natl Acad Sci U S A (2003) 1.11

Computational prediction of protein hot spot residues. Curr Pharm Des (2012) 1.11

Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization. Nucleic Acids Res (2005) 1.11

3dSS: 3D structural superposition. Nucleic Acids Res (2006) 1.10

Molecular dynamics studies of a DNA-binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor. Protein Sci (1992) 1.10

Oil/water transfer is partly driven by molecular shape, not just size. J Am Chem Soc (2010) 1.09

Profile analysis: detection of distantly related proteins. Proc Natl Acad Sci U S A (1987) 29.26

Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci U S A (1999) 22.80

Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J (1985) 20.39

Detecting protein function and protein-protein interactions from genome sequences. Science (1999) 18.69

A method to identify protein sequences that fold into a known three-dimensional structure. Science (1991) 14.08

Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J Mol Biol (1984) 13.69

Assessment of protein models with three-dimensional profiles. Nature (1992) 12.64

Tests for comparing related amino-acid sequences. Cytochrome c and cytochrome c 551 . J Mol Biol (1971) 12.21

Analysis of gene duplication repeats in the myosin rod. J Mol Biol (1983) 11.12

DIP: the database of interacting proteins. Nucleic Acids Res (2000) 10.06

Codon preference and its use in identifying protein coding regions in long DNA sequences. Nucleic Acids Res (1982) 9.99

A combined algorithm for genome-wide prediction of protein function. Nature (1999) 9.99

Profile analysis. Methods Enzymol (1990) 9.40

Three-dimensional structure of membrane and surface proteins. Annu Rev Biochem (1984) 7.38

The hydrophobic moment detects periodicity in protein hydrophobicity. Proc Natl Acad Sci U S A (1984) 6.36

Protein interaction databases. Curr Opin Biotechnol (2001) 5.22

Mining literature for protein-protein interactions. Bioinformatics (2001) 5.18

Aggressive lipid-lowering therapy compared with angioplasty in stable coronary artery disease. Atorvastatin versus Revascularization Treatment Investigators. N Engl J Med (1999) 5.09

The helical hydrophobic moment: a measure of the amphiphilicity of a helix. Nature (1982) 5.01

3D domain swapping: a mechanism for oligomer assembly. Protein Sci (1995) 4.96

Tropomyosin coiled-coil interactions: evidence for an unstaggered structure. J Mol Biol (1975) 4.79

Path of the polypeptide in bacteriorhodopsin. Proc Natl Acad Sci U S A (1980) 4.76

Ferricytochrome c. I. General features of the horse and bonito proteins at 2.8 A resolution. J Biol Chem (1971) 4.75

Domain swapping: entangling alliances between proteins. Proc Natl Acad Sci U S A (1994) 4.20

Periodic charge distributions in the myosin rod amino acid sequence match cross-bridge spacings in muscle. Nature (1982) 3.95

The crystal structure of diphtheria toxin. Nature (1992) 3.80

Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure. J Mol Biol (1983) 3.78

Profile scanning for three-dimensional structural patterns in protein sequences. Comput Appl Biosci (1988) 3.66

Gene duplications in the structural evolution of chymotrypsin. J Mol Biol (1979) 3.50

DIP: The Database of Interacting Proteins: 2001 update. Nucleic Acids Res (2001) 3.38

Periodic features in the amino acid sequence of nematode myosin rod. J Mol Biol (1983) 3.25

The 14-fold periodicity in alpha-tropomyosin and the interaction with actin. J Mol Biol (1976) 3.23

The structure of melittin. II. Interpretation of the structure. J Biol Chem (1982) 3.22

Atomic solvation parameters applied to molecular dynamics of proteins in solution. Protein Sci (1992) 3.05

Novel subunit-subunit interactions in the structure of glutamine synthetase. Nature (1986) 2.87

Alternative therapies used by women with breast cancer in four ethnic populations. J Natl Cancer Inst (2000) 2.87

Finding families for genomic ORFans. Bioinformatics (1999) 2.76

Hydrophobic organization of membrane proteins. Science (1989) 2.74

Sequence-structure analysis of FAD-containing proteins. Protein Sci (2001) 2.73

Crystal structure of defensin HNP-3, an amphiphilic dimer: mechanisms of membrane permeabilization. Science (1991) 2.71

A census of protein repeats. J Mol Biol (1999) 2.70

Protein fold recognition using sequence-derived predictions. Protein Sci (1996) 2.70

Randomized trial comparing traditional Chinese medical acupuncture, therapeutic massage, and self-care education for chronic low back pain. Arch Intern Med (2001) 2.67

A cDNA that suppresses MPP+ toxicity encodes a vesicular amine transporter. Cell (1992) 2.58

A method for measuring the non-random bias of a codon usage table. Nucleic Acids Res (1984) 2.57

Where metal ions bind in proteins. Proc Natl Acad Sci U S A (1990) 2.56

The structure of melittin in the form I crystals and its implication for melittin's lytic and surface activities. Biophys J (1982) 2.50

Sequence comparison by exponentially-damped alignment. Nucleic Acids Res (1984) 2.50

Use of complementary medicine by adult patients participating in cancer clinical trials. Oncol Nurs Forum (2000) 2.41

Crystal structure of human BPI and two bound phospholipids at 2.4 angstrom resolution. Science (1997) 2.38

Localizing proteins in the cell from their phylogenetic profiles. Proc Natl Acad Sci U S A (2000) 2.24

Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. J Mol Biol (2001) 2.17

Oligomer formation by 3D domain swapping: a model for protein assembly and misassembly. Adv Protein Chem (1997) 2.17

A domain-swapped RNase A dimer with implications for amyloid formation. Nat Struct Biol (2001) 2.15

Evidence for a repeating cross-beta sheet structure in the adenovirus fibre. EMBO J (1983) 2.09

Crystal structure of a synthetic triple-stranded alpha-helical bundle. Science (1993) 2.09

B29: a member of the immunoglobulin gene superfamily exclusively expressed on beta-lineage cells. Proc Natl Acad Sci U S A (1988) 2.05

The structure of melittin. I. Structure determination and partial refinement. J Biol Chem (1982) 2.04

Transproteomic evidence of a loop-deletion mechanism for enhancing protein thermostability. J Mol Biol (1999) 2.03

Paramyosin gene (unc-15) of Caenorhabditis elegans. Molecular cloning, nucleotide sequence and models for thick filament structure. J Mol Biol (1989) 1.94

Bioinformatic identification of potential autocrine signaling loops in cancers from gene expression profiles. Nat Genet (2001) 1.93

Secondary structure-based profiles: use of structure-conserving scoring tables in searching protein sequence databases for structural similarities. Proteins (1991) 1.88

Refined structure of dimeric diphtheria toxin at 2.0 A resolution. Protein Sci (1994) 1.88

Solution structure of protegrin-1, a broad-spectrum antimicrobial peptide from porcine leukocytes. Chem Biol (1996) 1.87

Reconstruction of glutamine synthetase using computer averaging. Ultramicroscopy (1978) 1.85

An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function. Proc Natl Acad Sci U S A (1994) 1.83

Crystal structure of diphtheria toxin bound to nicotinamide adenine dinucleotide. Biochemistry (1996) 1.81

Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium. Proc Natl Acad Sci U S A (1997) 1.81

Refined atomic model of glutamine synthetase at 3.5 A resolution. J Biol Chem (1989) 1.81

Interactions of melittin, a preprotein model, with detergents. Biochemistry (1979) 1.80

Assessing the performance of fold recognition methods by means of a comprehensive benchmark. Pac Symp Biocomput (1996) 1.75

A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence. J Mol Biol (1997) 1.72

Gene segments encoding transmembrane carboxyl termini of immunoglobulin gamma chains. Cell (1981) 1.65

Refined structure of monomeric diphtheria toxin at 2.3 A resolution. Protein Sci (1994) 1.64

The crystal structure of a 3D domain-swapped dimer of RNase A at a 2.1-A resolution. Proc Natl Acad Sci U S A (1998) 1.59

Rationale of the diet-heart statement of the American Heart Association. Report of the Nutrition Committee. Circulation (1993) 1.58

Repeating sequences and gene duplication in proteins. J Mol Biol (1972) 1.58

Assigning amino acid sequences to 3-dimensional protein folds. FASEB J (1996) 1.49

The structure of form I crystals of D-ribulose-1,5-diphosphate carboxylase. J Mol Biol (1975) 1.48

Sequence repeats in alpha-tropomyosin. J Mol Biol (1975) 1.46

Three-dimensional profiles from residue-pair preferences: identification of sequences with beta/alpha-barrel fold. Proc Natl Acad Sci U S A (1993) 1.45

Coiled coil formation and sequence regularities in the helical regions of alpha-keratin. J Mol Biol (1978) 1.45

Design of three-dimensional domain-swapped dimers and fibrous oligomers. Proc Natl Acad Sci U S A (2001) 1.45

Crystal structure of alpha 1: implications for protein design. Science (1990) 1.44

Crystal structure of the unactivated form of ribulose-1,5-bisphosphate carboxylase/oxygenase from tobacco refined at 2.0-A resolution. J Biol Chem (1992) 1.44

Defensins promote fusion and lysis of negatively charged membranes. Protein Sci (1993) 1.43

"Homology" in proteins and nucleic acids: a terminology muddle and a way out of it. Cell (1987) 1.42

The crystal structure of the designed trimeric coiled coil coil-VaLd: implications for engineering crystals and supramolecular assemblies. Protein Sci (1997) 1.42

Melittin forms crystals which are suitable for high resolution X-ray structural analysis and which reveal a molecular 2-fold axis of symmetry. J Biol Chem (1980) 1.40

An interfacial mechanism and a class of inhibitors inferred from two crystal structures of the Mycobacterium tuberculosis 30 kDa major secretory protein (Antigen 85B), a mycolyl transferase. J Mol Biol (2001) 1.40

Structural implications of the myosin amino acid sequence. Annu Rev Biophys Bioeng (1984) 1.39

pH-dependent insertion of proteins into membranes: B-chain mutation of diphtheria toxin that inhibits membrane translocation, Glu-349----Lys. Proc Natl Acad Sci U S A (1992) 1.33

The double helix coiled coil structure of murein lipoprotein from Escherichia coli. J Mol Biol (1978) 1.31

Packing in a new crystalline form of glutamine synthetase from Escherichia coli. J Mol Biol (1976) 1.30

Periodic charge distribution in the intermediate filament proteins desmin and vimentin. J Mol Biol (1982) 1.30

Fourteen actin-binding sites on tropomyosin? Nature (1975) 1.29

Caenorhabditis elegans embryos contain only one major species of Ro RNP. RNA (1995) 1.28

Aneurysm of the rabbit common carotid artery induced by periarterial application of calcium chloride in vivo. J Clin Invest (1988) 1.27