Published in Proc Natl Acad Sci U S A on December 07, 1999
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics (2013) 11.01
Computational study of protein specificity: the molecular basis of HIV-1 protease drug resistance. Proc Natl Acad Sci U S A (2001) 1.58
Computer-aided antibody design. Protein Eng Des Sel (2012) 1.44
Thermodynamic basis for promiscuity and selectivity in protein-protein interactions: PDZ domains, a case study. J Am Chem Soc (2006) 1.27
Molecular dynamics study of the energetic, mechanistic, and structural implications of a closed phosphate tube in ncd. Biophys J (2001) 1.14
Molecular dynamics simulations of galectin-1-oligosaccharide complexes reveal the molecular basis for ligand diversity. Proteins (2003) 1.09
Differences in electrostatic properties at antibody-antigen binding sites: implications for specificity and cross-reactivity. Biophys J (2002) 1.03
Oroxylin A inhibits hemolysis via hindering the self-assembly of α-hemolysin heptameric transmembrane pore. PLoS Comput Biol (2013) 1.02
Molecular dynamics studies of the HIV-1 TAR and its complex with argininamide. Nucleic Acids Res (2000) 0.96
A computational analysis of binding modes and conformation changes of MDM2 induced by p53 and inhibitor bindings. J Comput Aided Mol Des (2013) 0.95
A classical and ab initio study of the interaction of the myosin triphosphate binding domain with ATP. Biophys J (2002) 0.92
Mutational analysis of 48G7 reveals that somatic hypermutation affects both antibody stability and binding affinity. J Am Chem Soc (2013) 0.91
Molecular dynamics and binding specificity analysis of the bovine immunodeficiency virus BIV Tat-TAR complex. Biophys J (2001) 0.90
Crystal structure of the Leishmania major peroxidase-cytochrome c complex. Proc Natl Acad Sci U S A (2012) 0.90
Improving the species cross-reactivity of an antibody using computational design. Bioorg Med Chem Lett (2009) 0.90
Modeling DNA polymerase μ motions: subtle transitions before chemistry. Biophys J (2010) 0.89
Simulating structural and thermodynamic properties of carcinogen-damaged DNA. Biophys J (2003) 0.89
Comparison between Generalized-Born and Poisson-Boltzmann methods in physics-based scoring functions for protein structure prediction. J Mol Model (2005) 0.88
Energetic basis for drug resistance of HIV-1 protease mutants against amprenavir. J Comput Aided Mol Des (2012) 0.88
Phenol red interacts with the protofibril-like oligomers of an amyloidogenic hexapeptide NFGAIL through both hydrophobic and aromatic contacts. Biophys J (2006) 0.87
Context-dependent mutations predominate in an engineered high-affinity single chain antibody fragment. Protein Sci (2006) 0.86
Controlling the aggregation and rate of release in order to improve insulin formulation: molecular dynamics study of full-length insulin amyloid oligomer models. J Mol Model (2011) 0.84
Unique example of amyloid aggregates stabilized by main chain H-bond instead of the steric zipper: molecular dynamics study of the amyloidogenic segment of amylin wild-type and mutants. J Mol Model (2011) 0.83
A molecular dynamics study and free energy analysis of complexes between the Mlc1p protein and two IQ motif peptides. Biophys J (2006) 0.81
Molecular mechanism of the enhanced virulence of 2009 pandemic influenza A (H1N1) virus from D222G mutation in the hemagglutinin: a molecular modeling study. J Mol Model (2012) 0.80
Extracellular vimentin interacts with insulin-like growth factor 1 receptor to promote axonal growth. Sci Rep (2015) 0.79
Computer-assisted combinatorial design of bicyclic thymidine analogs as inhibitors of Mycobacterium tuberculosis thymidine monophosphate kinase. J Comput Aided Mol Des (2010) 0.79
DNA pol λ's extraordinary ability to stabilize misaligned DNA. J Am Chem Soc (2010) 0.78
Study of a ligand complexed with Cdk2/Cdk4 by computer simulation. J Mol Model (2005) 0.77
Relative free energy of binding between antimicrobial peptides and SDS or DPC micelles. Mol Simul (2009) 0.77
Does a diol cyclic urea inhibitor of HIV-1 protease bind tighter than its corresponding alcohol form? A study by free energy perturbation and continuum electrostatics calculations. J Comput Aided Mol Des (2001) 0.76
EGAR, A Food Protein-Derived Tetrapeptide, Reduces Seizure Activity in Pentylenetetrazole-Induced Epilepsy Models Through α-Amino-3-Hydroxy-5-Methyl-4-Isoxazole Propionate Receptors. Neurotherapeutics (2016) 0.75
Cas9-catalyzed DNA Cleavage Generates Staggered Ends: Evidence from Molecular Dynamics Simulations. Sci Rep (2016) 0.75
A non-canonical binding interface in the crystal structure of HIV-1 gp120 core in complex with CD4. Sci Rep (2017) 0.75
Exploring interaction of TNF and orthopoxviral CrmB protein by surface plasmon resonance and free energy calculation. Protein Pept Lett (2014) 0.75
Ab initio base fragment molecular orbital studies of influenza viral hemagglutinin HA1 full-domains in complex with sialoside receptors. J Mol Genet Med (2008) 0.75
Defining the complementarities between antibodies and haptens to refine our understanding and aid the prediction of a successful binding interaction. BMC Biotechnol (2015) 0.75
Detection of persistent organic pollutants binding modes with androgen receptor ligand binding domain by docking and molecular dynamics. BMC Struct Biol (2013) 0.75
Understanding the recognition mechanisms of Zα domain of human editing enzyme ADAR1 (hZα(ADAR1)) and various Z-DNAs from molecular dynamics simulation. J Mol Model (2014) 0.75
Somatic generation of antibody diversity. Nature (1983) 28.06
Reduced surface: an efficient way to compute molecular surfaces. Biopolymers (1996) 10.62
Electrostatic interactions in macromolecules: theory and applications. Annu Rev Biophys Biophys Chem (1990) 7.40
Cell selection by antigen in the immune response. Adv Immunol (1969) 6.05
Antibody diversity: somatic hypermutation of rearranged VH genes. Cell (1981) 4.65
Structural insights into the evolution of an antibody combining site. Science (1997) 3.92
A new method for predicting binding affinity in computer-aided drug design. Protein Eng (1994) 3.79
Calculation of electrostatic potentials in an enzyme active site. Nature (1987) 2.88
The immunological evolution of catalysis. Science (1996) 2.44
Salt effects on ligand-DNA binding. Minor groove binding antibiotics. J Mol Biol (1994) 2.27
Salt effects on protein-DNA interactions. The lambda cI repressor and EcoRI endonuclease. J Mol Biol (1994) 1.75
Ligand binding affinity prediction by linear interaction energy methods. J Comput Aided Mol Des (1998) 1.58
Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution. J Biomol Struct Dyn (1998) 1.48
Electrostatic fields in antibodies and antibody/antigen complexes. Prog Biophys Mol Biol (1992) 1.31
Immunological origins of binding and catalysis in a Diels-Alderase antibody. Science (1998) 1.28
What determines the van der Waals coefficient beta in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations? Proteins (1999) 1.21
Empirical free energy calculations: a blind test and further improvements to the method. J Mol Biol (1997) 1.18
Electrostatic interactions in hirudin-thrombin binding. Biophys Chem (1996) 1.09
Crystal structures of the free and liganded form of an esterolytic catalytic antibody. J Mol Biol (1997) 0.91
Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res (2000) 10.78
Boron nitride substrates for high-quality graphene electronics. Nat Nanotechnol (2010) 9.72
Linkage group I: the simultaneous estimation of recombination and interference. Birth Defects Orig Artic Ser (1976) 8.63
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science (1998) 8.46
Mutations in T-cell antigen receptor genes alpha and beta block thymocyte development at different stages. Nature (1992) 7.66
Control of memory formation through regulated expression of a CaMKII transgene. Science (1996) 7.56
Therapeutic benefit of intravenous administration of bone marrow stromal cells after cerebral ischemia in rats. Stroke (2001) 6.61
Leptin-regulated endocannabinoids are involved in maintaining food intake. Nature (2001) 6.36
New Ballard Score, expanded to include extremely premature infants. J Pediatr (1991) 5.82
Tumor necrosis factor receptor family member RANK mediates osteoclast differentiation and activation induced by osteoprotegerin ligand. Proc Natl Acad Sci U S A (1999) 5.78
Abbreviated regimens of zidovudine prophylaxis and perinatal transmission of the human immunodeficiency virus. N Engl J Med (1998) 5.65
The TAF(II)250 subunit of TFIID has histone acetyltransferase activity. Cell (1996) 5.20
A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. J Biomol Struct Dyn (1999) 5.14
Phosphatidylinositol 3-kinase activation is required for insulin stimulation of pp70 S6 kinase, DNA synthesis, and glucose transporter translocation. Mol Cell Biol (1994) 5.13
Effect of isoniazid on the in vivo mycolic acid synthesis, cell growth, and viability of Mycobacterium tuberculosis. Antimicrob Agents Chemother (1972) 4.64
Intravenous administration of human umbilical cord blood reduces behavioral deficits after stroke in rats. Stroke (2001) 4.64
Human marrow stromal cell therapy for stroke in rat: neurotrophins and functional recovery. Neurology (2002) 4.45
A dust-obscured massive maximum-starburst galaxy at a redshift of 6.34. Nature (2013) 4.43
An integrated genomic analysis of lung cancer reveals loss of DUSP4 in EGFR-mutant tumors. Oncogene (2009) 4.10
Peptoids: a modular approach to drug discovery. Proc Natl Acad Sci U S A (1992) 4.08
Effect of mobile phone intervention for diabetes on glycaemic control: a meta-analysis. Diabet Med (2011) 4.04
Hippocampal morphometry in schizophrenia by high dimensional brain mapping. Proc Natl Acad Sci U S A (1998) 3.72
The diversity of the DnaJ/Hsp40 family, the crucial partners for Hsp70 chaperones. Cell Mol Life Sci (2006) 3.62
Rare structural variants found in attention-deficit hyperactivity disorder are preferentially associated with neurodevelopmental genes. Mol Psychiatry (2009) 3.56
National character does not reflect mean personality trait levels in 49 cultures. Science (2005) 3.56
Is routine indwelling catheterisation of the bladder for caesarean section necessary? A systematic review. BJOG (2010) 3.54
Ballistic 2-d imaging through scattering walls using an ultrafast optical kerr gate. Science (1991) 3.53
In vitro activation of CPP32 and Mch3 by Mch4, a novel human apoptotic cysteine protease containing two FADD-like domains. Proc Natl Acad Sci U S A (1996) 3.53
Severe B cell hyperplasia and autoimmune disease in TALL-1 transgenic mice. Proc Natl Acad Sci U S A (2000) 3.37
The maximal affinity of ligands. Proc Natl Acad Sci U S A (1999) 3.24
Preclinical detection of Alzheimer's disease: hippocampal shape and volume predict dementia onset in the elderly. Neuroimage (2005) 3.21
Shortened telomeres in the expanded CD28-CD8+ cell subset in HIV disease implicate replicative senescence in HIV pathogenesis. AIDS (1996) 2.95
BRCA1 is associated with a human SWI/SNF-related complex: linking chromatin remodeling to breast cancer. Cell (2000) 2.94
Crucial role of the interleukin 1 receptor family member T1/ST2 in T helper cell type 2-mediated lung mucosal immune responses. J Exp Med (1999) 2.92
Therapeutic benefit of intracerebral transplantation of bone marrow stromal cells after cerebral ischemia in rats. J Neurol Sci (2001) 2.84
Efficacy and safety of adeno-associated viral vectors based on serotype 8 and 9 vs. lentiviral vectors for hemophilia B gene therapy. J Thromb Haemost (2006) 2.81
BRAF screening as a low-cost effective strategy for simplifying HNPCC genetic testing. J Med Genet (2004) 2.75
Arrays of complementary oligonucleotides for analysing the hybridisation behaviour of nucleic acids. Nucleic Acids Res (1994) 2.75
BAFF binds to the tumor necrosis factor receptor-like molecule B cell maturation antigen and is important for maintaining the peripheral B cell population. J Exp Med (2000) 2.69
Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution. J Mol Biol (1996) 2.66
An oncogenic role of sphingosine kinase. Curr Biol (2000) 2.59
Tissue plasminogen activator (tPA) deficiency exacerbates cerebrovascular fibrin deposition and brain injury in a murine stroke model: studies in tPA-deficient mice and wild-type mice on a matched genetic background. Arterioscler Thromb Vasc Biol (1999) 2.56
Alteration of deposition pattern and pulmonary response as a result of improved dispersion of aspirated single-walled carbon nanotubes in a mouse model. Am J Physiol Lung Cell Mol Physiol (2007) 2.55
Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA. J Am Chem Soc (2001) 2.55
Spinal cord atrophy and disability in multiple sclerosis. A new reproducible and sensitive MRI method with potential to monitor disease progression. Brain (1996) 2.54
Spinal cord injury in rat: treatment with bone marrow stromal cell transplantation. Neuroreport (2000) 2.49
Interactions of the 5-hydroxytryptamine 3 antagonist class of antiemetic drugs with human cardiac ion channels. J Pharmacol Exp Ther (2000) 2.47
Mch3, a novel human apoptotic cysteine protease highly related to CPP32. Cancer Res (1995) 2.47
Hybrid vectors based on adeno-associated virus serotypes 2 and 5 for muscle-directed gene transfer. J Virol (2001) 2.46
DNA microarray-based identification of genes controlled by autoinducer 2-stimulated quorum sensing in Escherichia coli. J Bacteriol (2001) 2.40
Characterization of physical interactions of the putative transcriptional adaptor, ADA2, with acidic activation domains and TATA-binding protein. J Biol Chem (1995) 2.37
Electrostatic recognition between superoxide and copper, zinc superoxide dismutase. Nature (1984) 2.36
What are covering doctors told about their patients? Analysis of sign-out among internal medicine house staff. Qual Saf Health Care (2009) 2.35
Epidemiological link between exposure to poultry and all influenza A(H7N9) confirmed cases in Huzhou city, China, March to May 2013. Euro Surveill (2013) 2.34
Early DAT is distinguished from aging by high-dimensional mapping of the hippocampus. Dementia of the Alzheimer type. Neurology (2000) 2.31
Identification of human proteins functionally conserved with the yeast putative adaptors ADA2 and GCN5. Mol Cell Biol (1996) 2.30
Molecular characterization of Streptococcus pneumoniae type 4, 6B, 8, and 18C capsular polysaccharide gene clusters. Infect Immun (2001) 2.28
CARD11 and CARD14 are novel caspase recruitment domain (CARD)/membrane-associated guanylate kinase (MAGUK) family members that interact with BCL10 and activate NF-kappa B. J Biol Chem (2001) 2.25
Molecular dynamics simulation of nucleic acids. Annu Rev Phys Chem (2000) 2.21
Tandem genes encode cell-surface polypeptides SspA and SspB which mediate adhesion of the oral bacterium Streptococcus gordonii to human and bacterial receptors. Mol Microbiol (1996) 2.21
Submillimetre galaxies reside in dark matter haloes with masses greater than 3 × 10(11) solar masses. Nature (2011) 2.21
Lamivudine in late pregnancy to prevent perinatal transmission of hepatitis B virus infection: a multicentre, randomized, double-blind, placebo-controlled study. J Viral Hepat (2008) 2.19
Effects of N-(4-hydroxyphenyl)retinamide on hTERT expression in the bronchial epithelium of cigarette smokers. J Natl Cancer Inst (2001) 2.18
T cell-derived IL-10 antagonizes macrophage function in mycobacterial infection. J Immunol (1997) 2.18
Ginsenoside-Rd improves outcome of acute ischaemic stroke - a randomized, double-blind, placebo-controlled, multicenter trial. Eur J Neurol (2012) 2.18
The pharmacogenetics research network: from SNP discovery to clinical drug response. Clin Pharmacol Ther (2007) 2.18
Airway smooth muscle dynamics: a common pathway of airway obstruction in asthma. Eur Respir J (2007) 2.16
Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches. Proteins (1993) 2.13
Hofstadter's butterfly and the fractal quantum Hall effect in moiré superlattices. Nature (2013) 2.13
Detection of genetic variation with radioactive ligands. III. genetic polymorphism of transcobalamin II in human plasma. Am J Hum Genet (1978) 2.13
A systematic approach for detecting high-frequency restriction fragment length polymorphisms using large genomic probes. Am J Hum Genet (1985) 2.12
DNA computing on surfaces. Nature (2000) 2.11
Economic burden of smoking in China, 2000. Tob Control (2006) 2.08
What happens when the patent ductus arteriosus is treated less aggressively in very low birth weight infants? J Perinatol (2011) 2.08
The MITE family heartbreaker (Hbr): molecular markers in maize. Proc Natl Acad Sci U S A (2000) 2.08
The Ced-3/interleukin 1beta converting enzyme-like homolog Mch6 and the lamin-cleaving enzyme Mch2alpha are substrates for the apoptotic mediator CPP32. J Biol Chem (1996) 2.07
Restriction and enhancement of human immunodeficiency virus type 1 replication by modulation of intracellular deoxynucleoside triphosphate pools. J Virol (1994) 2.07
Intrastriatal transplantation of bone marrow nonhematopoietic cells improves functional recovery after stroke in adult mice. J Cereb Blood Flow Metab (2000) 2.06
Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. Annu Rev Biophys Biomol Struct (2001) 2.06
Calculation of the relative change in binding free energy of a protein-inhibitor complex. Science (1987) 2.04
Mapping oligonucleotides of Rous sarcoma virus RNA that segregate with polymerase and group-specific antigen markers in recombinants. Proc Natl Acad Sci U S A (1976) 2.04
Synergistic interaction between leptin and cholecystokinin to reduce short-term food intake in lean mice. Proc Natl Acad Sci U S A (1997) 2.04
Tumor necrosis factor-alpha induces adhesion molecule expression through the sphingosine kinase pathway. Proc Natl Acad Sci U S A (1998) 2.03
Target site selection for an RNA-cleaving catalytic DNA. Nat Biotechnol (1999) 2.03
Treatment of stroke in rat with intracarotid administration of marrow stromal cells. Neurology (2001) 2.02
Secondary sexual characteristics in boys: estimates from the national health and nutrition examination survey III, 1988-1994. Arch Pediatr Adolesc Med (2001) 2.02
Suppression of skin tumorigenesis in c-Jun NH(2)-terminal kinase-2-deficient mice. Cancer Res (2001) 2.00
Crystal structure and mechanism of histone acetylation of the yeast GCN5 transcriptional coactivator. Proc Natl Acad Sci U S A (1999) 1.99
Structure and mapping of the human beta-defensin HBD-2 gene and its expression at sites of inflammation. Gene (1998) 1.99
Salivary gland neoplasms in oral and maxillofacial regions: a 23-year retrospective study of 6982 cases in an eastern Chinese population. Int J Oral Maxillofac Surg (2009) 1.98
Free energy calculations by computer simulation. Science (1987) 1.98
Decreased interstitial cell of cajal volume in patients with slow-transit constipation. Gastroenterology (2000) 1.95
Rho kinases play an obligatory role in vertebrate embryonic organogenesis. Development (2001) 1.95
MR nerve imaging in a prospective cohort of patients with suspected carpal tunnel syndrome. Neurology (2002) 1.94
Gene expression in human alcoholism: microarray analysis of frontal cortex. Alcohol Clin Exp Res (2000) 1.93
Rat proteinase-activated receptor-2 (PAR-2): cDNA sequence and activity of receptor-derived peptides in gastric and vascular tissue. Br J Pharmacol (1996) 1.93
Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models. J Med Chem (2000) 1.92
Liver-derived CTL in hepatitis C virus infection: breadth and specificity of responses in a cohort of persons with chronic infection. J Immunol (1998) 1.92
Homologous DNA pairing promoted by a 20-amino acid peptide derived from RecA. Science (1996) 1.90