Published in J Comput Biol on January 01, 1995
Ideal architecture of residue packing and its observation in protein structures. Protein Sci (1997) 1.09
Protein secondary structure appears to be robust under in silico evolution while protein disorder appears not to be. Bioinformatics (2010) 0.98
Producing high-accuracy lattice models from protein atomic coordinates including side chains. Adv Bioinformatics (2012) 0.85
LocalMove: computing on-lattice fits for biopolymers. Nucleic Acids Res (2008) 0.82
How good are simplified models for protein structure prediction? Adv Bioinformatics (2014) 0.80
Reduced surface: an efficient way to compute molecular surfaces. Biopolymers (1996) 10.62
Automated docking of flexible ligands: applications of AutoDock. J Mol Recognit (1996) 6.51
Distributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4. J Comput Aided Mol Des (1996) 5.09
Automated docking of substrates to proteins by simulated annealing. Proteins (1990) 4.49
Structural symmetry and protein function. Annu Rev Biophys Biomol Struct (2000) 4.11
The reactivity of anti-peptide antibodies is a function of the atomic mobility of sites in a protein. Nature (1984) 4.05
A theoretical search for folding/unfolding nuclei in three-dimensional protein structures. Proc Natl Acad Sci U S A (1999) 3.02
Tomato bushy stunt virus at 2.9 A resolution. Nature (1978) 2.87
Structure, function and properties of antibody binding sites. J Mol Biol (1991) 2.84
Why do globular proteins fit the limited set of folding patterns? Prog Biophys Mol Biol (1987) 2.33
The classification and origins of protein folding patterns. Annu Rev Biochem (1990) 2.30
Theory of cooperative transitions in protein molecules. I. Why denaturation of globular protein is a first-order phase transition. Biopolymers (1989) 1.94
Theory of protein secondary structure and algorithm of its prediction. Biopolymers (1983) 1.78
Similarities of protein topologies: evolutionary divergence, functional convergence or principles of folding? Q Rev Biophys (1980) 1.76
Morphology of protein-protein interfaces. Structure (1998) 1.67
What is the probability of a chance prediction of a protein structure with an rmsd of 6 A? Fold Des (1998) 1.64
Structure of tomato busy stunt virus IV. The virus particle at 2.9 A resolution. J Mol Biol (1983) 1.64
Identification and analysis of the acyl carrier protein (ACP) docking site on beta-ketoacyl-ACP synthase III. J Biol Chem (2000) 1.54
The atomic mobility component of protein antigenicity. Annu Rev Immunol (1985) 1.40
Shape analysis of molecular surfaces. Biopolymers (1993) 1.27
Soluble proteins: size, shape and function. Trends Biochem Sci (1993) 1.22
Comparison of predicted and experimentally determined secondary structure of adenyl kinase. Nature (1974) 1.21
Theory of cooperative transitions in protein molecules. II. Phase diagram for a protein molecule in solution. Biopolymers (1989) 1.20
General architecture of the alpha-helical globule. J Mol Biol (1988) 1.19
Viral evolution in response to the broad-based retroviral protease inhibitor TL-3. J Virol (2001) 1.03
Approximation and characterization of molecular surfaces. Biopolymers (1993) 1.03
Modelling of factor Xa-inhibitor complexes: a computational flexible docking approach. Proteins (1999) 1.01
Recognition and interactions controlling the assemblies of beta barrel domains. Biophys J (1986) 0.99
Electrostatic orientation of the electron-transfer complex between plastocyanin and cytochrome c. J Biol Chem (1991) 0.98
Analysis of a data set of paired uncomplexed protein structures: new metrics for side-chain flexibility and model evaluation. Proteins (2001) 0.95
Folding nuclei in proteins. FEBS Lett (2001) 0.95
Alteration of substrate and inhibitor specificity of feline immunodeficiency virus protease. J Virol (2000) 0.94
Molecular analysis of the feline immunodeficiency virus protease: generation of a novel form of the protease by autoproteolysis and construction of cleavage-resistant proteases. J Virol (1997) 0.94
De novo design, synthesis and study of albebetin, a polypeptide with a predetermined three-dimensional structure. Probing the structure at the nanogram level. J Mol Biol (1992) 0.93
Folding of circular permutants with decreased contact order: general trend balanced by protein stability. J Mol Biol (2001) 0.93
Residue-residue mean-force potentials for protein structure recognition. Protein Eng (1997) 0.93
Optimization of protein structure on lattices using a self-consistent field approach. J Comput Biol (1998) 0.93
Automated docking in crystallography: analysis of the substrates of aconitase. Proteins (1993) 0.92
Accurate general method for lattice approximation of three-dimensional structure of a chain molecule. Proteins (1995) 0.92
Revisiting catalysis by chymotrypsin family serine proteases using peptide substrates and inhibitors with unnatural main chains. J Biol Chem (1999) 0.92
Statistical significance of protein structure prediction by threading. Proc Natl Acad Sci U S A (2000) 0.91
Predicted beta-structure stability parameters under experimental test. Protein Eng (1995) 0.91
Averaging interaction energies over homologs improves protein fold recognition in gapless threading. Proteins (1999) 0.91
Structural studies of FIV and HIV-1 proteases complexed with an efficient inhibitor of FIV protease. Proteins (2000) 0.90
Integrating computation and visualization for biomolecular analysis: an example using python and AVS. Pac Symp Biocomput (1999) 0.89
Folding rate dependence on the chain length of RNA-like heteropolymers. Fold Des (1998) 0.87
A theory of protein molecule self-organization. IV. Helical and irregular local structures of unfolded protein chains. J Mol Biol (1976) 0.87
Theoretical study of a landscape of protein folding-unfolding pathways. Folding rates at midtransition. Biochemistry (2001) 0.86
Recognition of protein structure on coarse lattices with residue-residue energy functions. Protein Eng (1997) 0.84
Recognition templates for predicting adenylate-binding sites in proteins. J Mol Biol (2001) 0.84
Protein design on computers. Five new proteins: Shpilka, Grendel, Fingerclasp, Leather, and Aida. Proteins (1992) 0.84
Building self-avoiding lattice models of proteins using a self-consistent field optimization. Proteins (1996) 0.83
Ionization state and molecular docking studies for the macrophage migration inhibitory factor: the role of lysine 32 in the catalytic mechanism. J Mol Recognit (2000) 0.83
Theory of protein molecule self-organization. I. Thermodynamic parameters of local secondary structures in the unfolded protein chain. Biopolymers (1977) 0.82
Statistical analysis of the correlation among amino acid residues in helical, beta-structural and non-regular regions of globular proteins. J Mol Biol (1971) 0.82
Principal folding pathway and topology of all-beta proteins. FEBS Lett (1979) 0.82
Prediction of protein secondary structure based on physical theory. Histones. Protein Eng (1989) 0.82
[The brain in stereotaxic coordinates (a textbook for colleges)]. Zh Vyssh Nerv Deiat Im I P Pavlova (1994) 0.81
Search for the most stable folds of protein chains: II. Computation of stable architectures of beta-proteins using a self-consistent molecular field theory. Protein Eng (1996) 0.81
Coevolution and subsite decomposition for the design of resistance-evading HIV-1 protease inhibitors. J Mol Biol (1999) 0.81
Visualizing biological molecules. Sci Am (1992) 0.81
Cunning simplicity of protein folding landscapes. Protein Eng (2001) 0.80
Secondary structure of globular proteins at the early and the final stages in protein folding. FEBS Lett (1993) 0.80
Molecular illustration in black and white. J Mol Graph (1992) 0.80
Connexin 26 expression and extensive gap junctional coupling in cultures of GT1-7 cells secreting gonadotropin-releasing hormone. Neuroendocrinology (1999) 0.79
Theory of protein molecule self-organization. II. A comparison of calculated thermodynamic parameters of local secondary structures with experiments. Biopolymers (1977) 0.79
Docking of 4-oxalocrotonate tautomerase substrates: implications for the catalytic mechanism. Biopolymers (1999) 0.79
Configurational transitions in Fourier series-represented DNA supercoils. Biophys J (1997) 0.78
cI and lexA repressors consist of three cro-like domains. FEBS Lett (1982) 0.78
Recognition of signal sequences. FEBS Lett (1983) 0.78
Coevolutionary analysis of resistance-evading peptidomimetic inhibitors of HIV-1 protease. Proc Natl Acad Sci U S A (1999) 0.77
Folding of chains with random and edited sequences: similarities and differences. Protein Eng (1995) 0.77
Texture mapping parametric molecular surfaces. J Mol Graph (1995) 0.77
Approximation and visualization of large-scale motion of protein surfaces. J Mol Graph (1995) 0.77
Interactive modeling of supramolecular assemblies. J Mol Graph Model (1998) 0.77
Biomolecular visualization using AVS. J Mol Graph (1995) 0.77
Folding nuclei in 3D protein structures. Pac Symp Biocomput (2000) 0.77
Computational coevolution of antiviral drug resistance. Artif Life (1998) 0.77
A new approach to the design of a sequence with the highest affinity for a molecular surface. Protein Eng (1992) 0.76
Conditioned media from the injured lower vertebrate CNS promote neurite outgrowth from mammalian brain neurons in vitro. Brain Res (1987) 0.76
Inhibition of phosphorylcholine binding to antibodies using synthetic peptides. Nature (1987) 0.76
Transmembrane alpha-helices in the gap junction membrane channel: systematic search of packing models based on the pair potential function. Microsc Res Tech (2001) 0.76
How homologs can help to predict protein folds even though they cannot be predicted for individual sequences. J Comput Biol (1998) 0.76
[When and how can homologs overcome errors in the energy estimates and make the 3D structure prediction possible]. Biofizika (2000) 0.76
Theory of protein molecule self-organization. III. A calculating method for the probabilities of the secondary structure formation in an unfolded polypeptide chain. Biopolymers (1977) 0.75
[A rapid and precise method for lattice approximation of the course of a protein chain based on a dynamic programming algorithm]. Mol Biol (Mosk) (1995) 0.75
Prediction of the three-dimensional structure for ribosomal protein L25. FEBS Lett (1975) 0.75
Probes for double helical DNA sequence information: molecular mechanics study of a proposed model. J Biomol Struct Dyn (1987) 0.75
Accurate mean-force pairwise-residue potentials for discrimination of protein folds. Pac Symp Biocomput (1997) 0.75
S6 permutein shows that the unusual target topology is not responsible for the absence of rigid tertiary structure in de novo protein albebetin. FEBS Lett (1997) 0.75
Did the primitive ribosomal RNA code primitive ribosomal protein? FEBS Lett (1977) 0.75
Structural model for interferons. FEBS Lett (1985) 0.75
Search for the most stable folds of protein chains: III. Improvement in fold recognition by averaging over homologous sequences and 3D structures. Proteins (2000) 0.75
Serials standards work: the next frontier. Libr Resour Tech Serv (1990) 0.75
Derivation and testing residue-residue mean-force potentials for use in protein structure recognition. Methods Mol Biol (2000) 0.75