Index

A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z |

Symbols


1983 3.1.6.1, 3.1.6.2, 3.1.6.3 1995 3.1.6.35, 3.1.6.36, 3.1.6.37
1984 3.1.6.4, 3.1.6.5 1996 3.1.6.38, 3.1.6.39, 3.1.6.40, 3.1.6.41
1985 3.1.6.6 1997 3.1.6.42, 3.1.6.43, 3.1.6.44, 3.1.6.45, 3.1.6.46, 3.1.6.47, 3.1.6.48, 3.1.6.49, 3.1.6.50, 3.1.6.51, 3.1.6.52, 3.1.6.53
1988 3.1.6.7, 3.1.6.8, 3.1.6.9 1998 3.1.6.54, 3.1.6.55, 3.1.6.56, 3.1.6.57, 3.1.6.58, 3.1.6.59
1989 3.1.6.10, 3.1.6.11, 3.1.6.12, 3.1.6.13 1999 3.1.6.60, 3.1.6.61, 3.1.6.62, 3.1.6.63, 3.1.6.64, 3.1.6.65, 3.1.6.66, 3.1.6.67
1990 3.1.6.14, 3.1.6.15, 3.1.6.16, 3.1.6.17 2000 3.1.6.68, 3.1.6.69, 3.1.6.70, 3.1.6.71, 3.1.6.72, 3.1.6.73, 3.1.6.74
1991 3.1.6.18 2001 3.1.6.75, 3.1.6.76, 3.1.6.77, 3.1.6.78, 3.1.6.79
1992 3.1.6.19, 3.1.6.20, 3.1.6.21, 3.1.6.22 2002 3.1.6.80, 3.1.6.81, 3.1.6.82, 3.1.6.83
1993 3.1.6.23, 3.1.6.24, 3.1.6.25, 3.1.6.26, 3.1.6.27 3d model 2.4.6
1994 3.1.6.28, 3.1.6.29, 3.1.6.30, 3.1.6.31, 3.1.6.32, 3.1.6.33, 3.1.6.34

A


ab initio 2.1.1 analysis 3.1.6.5
Ab initio folding 3.1.6.60 Analysis 3.1.6.81
ab initio prediction 3.1.6.32 Analytical Molecular Surface 3.1.6.38
Abagyan 3.1.6.1, 3.1.6.11, 3.1.6.12, 3.1.6.13, 3.1.6.14, 3.1.6.15, 3.1.6.19, 3.1.6.2, 3.1.6.20, 3.1.6.21, 3.1.6.23, 3.1.6.28, 3.1.6.3, 3.1.6.30, 3.1.6.33, 3.1.6.4, 3.1.6.45, 3.1.6.46, 3.1.6.49, 3.1.6.51, 3.1.6.60, 3.1.6.7, 3.1.6.75 anchorage 3.1.6.59
ABP 3.1.6.59 Andrew Bordner 9.1.3
abstracts 3, 3.2 Andrew Orry 9.1.10
acceleration 3.1.6.6 Anomalous 3.1.6.8
Active Site CD59 3.1.6.44 Antibodies against TRAP 3.1.6.70
adenine-thymine 3.1.6.8 anticholera toxin antibody using internal coordinate mechanics 3.1.6.64
administrative 9.2 appearing 3.1.6.2
administrative assistant 9.1 applications 3.1.5
Algorithm 3.1.6.81 Argos 3.1.6.29
algorithms 2.4, 3.1.4 arrangement 3.1.6.3
aligned sequences 3.1.6.45 Array 3.1.6.81
alumni 9.2 articles 3
Aminoglycoside binding 3.1.6.71 assistant 9.1.12
AMPA 3.1.6.59 assistants 9.2
An integrated genetic linkage map 3.1.6.61 Automatic Search 3.1.6.12

B


B-Type Conformation 3.1.6.16 Bioorganic Chemistry 3.1.6.4
barrel structure stability 3.1.6.36 Biophysics 3.1.6.1, 3.1.6.2, 3.1.6.3
bee 6, 6.2 Biopolymers 3.1.6.16, 3.1.6.5, 3.1.6.79
beowulf 8 BMC Structural Biology Journal 3.1.6.77
Biased Probability Monte Carlo Conformational Searches 3.1.6.30 book chapters 3
binding energy for small molecules 3.1.6.63 Borchert 3.1.6.24, 3.1.6.31, 3.1.6.35
Biochemistry 3.1.6.47 boss 9.1, 9.1.1
Biofizika 3.1.6.22, 3.1.6.6 Brian Marsden 9.1.9
bioinformatics 2.2, 3.1.2 Brive 3.1.6.83
Biomolecular 3.1.6.10, 3.1.6.11

C


Calculation 3.1.6.4 Computer-Aided 3.1.6.10, 3.1.6.11
calendar 12 Computers & Chemistry 3.1.6.29, 3.1.6.68
calf thymus type I topoisomerase 3.1.6.17 Computers Chem 3.1.6.14
camptothecin 3.1.6.17 configure protein side-chains 3.1.6.25
Cardozo 3.1.6.37, 3.1.6.54, 3.1.6.68 Conformational 3.1.6.14, 3.1.6.5
cDNA 3.1.6.55 conformational energy 3.1.6.22
CED-4 3.1.6.54 conformational flexibility 3.1.6.35
Chain 3.1.6.7 Conformational Searches 3.1.6.19
Chalikian 3.1.6.39 conformational searches 3.1.6.20
characterization 3.1.6.31 conformations 3.1.6.4
chip 3.1.6.81 contact area difference 2.4.6
Chuprina 3.1.6.8, 3.1.6.9 Contact Area Difference 3.1.6.46
Claudio Cavasotto 9.1.5 Contour-Buildup Algorithm 3.1.6.38
cluster 8 convertase enzyme 3.1.6.55
collagen 3.1.6.3, 3.1.6.4 creation 3.1.6.31
collagen structure 3.1.6.5 cross correlating thermodynamic 3.1.6.39
Comparison 3.1.6.7 crystal structure 3.1.6.24
complement inhibitor CD59 3.1.6.47 Crystal Structure 3.1.6.53
compressibility measurements 3.1.6.39 current members 9.1
computer 8 Current Opinion in Chemical Biology 3.1.6.75
Computer Aided Innovation of New Materials 3.1.6.20 Cytokine & Growth Factor Reviews 3.1.6.41
Computer Simulation Biomolecular Systems 3.1.6.51

D


Deedee Bridgens 9.2.9 Diverse Functions 3.1.6.41
deformation zone mapping 3.1.6.49 DNA 3.1.6.9
Derivation 3.1.6.18, 3.1.6.65 DNA bending model 3.1.6.15
derivative calculations 3.1.6.34 DNA cleaving activity 3.1.6.17
design 2.3 DNA Sequences 3.1.6.13
Design 3.1.6.31 DNA-binding Domain 3.1.6.26
Determine Human CD59 Species Selective Activity 3.1.6.66 docking 2.3, 3.1.3, 3.1.6.59
diagram 4 Docking 3.1.6.80, 3.1.6.82
differential display 3.1.6.55 docking and structure prediction 3.1.6.33
Diffraction 3.1.6.1 Doklady Academii Nauk SSSR 3.1.6.13
diffraction 3.1.6.2 Domain Shared Between 3.1.6.54
Dimeric Peroxisomal 3.1.6.53 drug 2.3, 2.3.1
distant similarities 2.2.1 drug design 3.1.3
distantly related proteins 3.1.6.28 Drug-Receptor Thermodynamics Introduction and Applications 3.1.6.78
distorted native conformation 3.1.6.33 Dynamics 3.1.6.10, 3.1.6.11

E


effects 3.1.6.2 Energy strain 3.1.6.56
Efficient parallelization energy 3.1.6.34 engineered monomeric triosephosphate isomerase 3.1.6.24
Efficient stochastic global optimization 3.1.6.67 Estimating local backbone structural deviation 3.1.6.68
Eisenhaber 3.1.6.16 eucaryotic gene regulatory proteins 3.1.6.26
Eisenmenger 3.1.6.25 evaluate accuracy 3.1.6.46
Electrophoretic behaviour 3.1.6.15 Evaluating energetics empty cavities 3.1.6.52
Electrostatic Calculations 3.1.6.30 evaluation 2.4.6
Embo J 3.1.6.57 events 12
Emerging Group Proteins 3.1.6.41 Experimental Cell Research 3.1.6.74
encodes ubiquitin-conjugating enzyme homolog 3.1.6.48 Explicit Equations 3.1.6.18
energy calculations 3.1.6.28 expression active enzyme regulation 3.1.6.55
energy optimization problem 3.1.6.78 Expression Adenovirus Receptor 3.1.6.74

F


factor 3.1.6.6 Folding & Design 3.1.6.56
Fernandez-Recio 3.1.6.80, 3.1.6.82 Folding and Design 3.1.6.58
Fiber Knob 3.1.6.74 folding simulations 3.1.6.79
fibrils 3.1.6.3 Folds 3.1.6.7
Filikov 3.1.6.69 former 9.2, 9.2
finding few minimums 3.1.6.29 former interns 9.2
flexible 2.3 former members 9.2
flexible docking 3.1.3 Frederic Fleche 9.2.11
Flexible Proline Rings 3.1.6.14 fully conserved phosphateloop 3.1.6.76
flexible protein-ligand docking 2.3.1 fundings 2.5
Flexible protein-ligand docking 3.1.6.50

G


G-proteins 3.1.6.54 Genome Res 3.1.6.72
Gallery 4 Gibson 3.1.6.26
Gantt 3.1.6.70 global energy optimization 3.1.6.23, 3.1.6.50, 3.1.6.51
Gates 3.1.6.61 Global optimization 3.1.6.22
gaussian 6 global optimization 3.1.6.60
Gaussian 6.4 Globular Proteins 3.1.6.12
gene mutated 3.1.6.48 Goodman 3.1.6.41
General Patterns 3.1.6.13 graduate students 9.2
Genetic linkage mapping 3.1.6.72 grants 2.5
genetic text 3.1.6.6 Gromova 3.1.6.17
Genome Research 9 3.1.6.61 group publications 3

H


helical 3.1.6.2 homology modeling 3.1.6.25
Helices 3.1.6.12 Homology modeling 3.1.6.37, 3.1.6.49
helix 3.1.6.1 homology models 3.1.6.68
Helix-Loop-Helix family 3.1.6.26 Houbrechts 3.1.6.36
High-Density 3.1.6.81 human arthritis-affected cartilage 3.1.6.55
High-throughput Docking 3.1.6.75 human breast cancer 3.1.6.48
HIV-1 TAR 3.1.6.69 hydration of globular proteins 3.1.6.39
Home 1 Hydration Shells 3.1.6.16
homology 5 Hyuk Soon Choi 9.1.11

I


ICM 3.1.6.33, 3.1.6.49 inhibit Plasmodium sporozoite infectivity in vivo 3.1.6.70
icm 6, 6.1 Integral Distribution 3.1.6.81
ICM Build Model Web Interface 5.3 Interaction 3.1.6.13, 3.1.6.74
ICM method 3.1.6.37 internal coordinate mechanics 3.1.6.34
Identification analysis 3.1.6.57 Internal Coordinates 3.1.6.18
Identification Individual Residues 3.1.6.66 internal coordinates 3.1.6.50
Identification Ligands RNA targets structure-based virtual screening 3.1.6.69 internal mutations proteins 3.1.6.52
identifying atoms 3.1.6.27 internship 9.2.11
improvement 3.1.6.6 internships 9.1
improvements 3.1.6.49 Isakoff 3.1.6.57
in press 3.1.6.83 Isolation 3.1.6.55
In Silico Discovery 3.1.6.77 Ivanitskii 3.1.6.6
Infection and Immunity 3.1.6.70

J


J Biomol Struct Dyn 3.1.6.10, 3.1.6.11, 3.1.6.12, 3.1.6.7 J Struct Biol 3.1.6.38
J Comp Chem 3.1.6.33, 3.1.6.34 J
J Comput Phys 3.1.6.18      Biomol Struct Dyn 3.1.6.9
J Expt Medicine 3.1.6.44 JBiolChem 3.1.6.66
J Mol Biol 3.1.6.19, 3.1.6.25, 3.1.6.30, 3.1.6.39, 3.1.6.45, 3.1.6.46, 3.1.6.53, 3.1.6.71 JCAMD 3.1.6.69
J Mol Graph 3.1.6.27 Jianghong An 9.1.2
J Molecular Recognition 3.1.6.63 Jin 3.1.6.71
J of Immunology 3.1.6.55 Journal of Computational Physics 3.1.6.60
J of Mol Model 3.1.6.54 Juan Fernandez-Recio 9.1.7

K


Kaisheng Chen 9.2.5 Kelly 3.1.6.72
Kathleen Vanderbur 9.1.12 Koonin 3.1.6.48
kathy 9.1.12 Kuznetsov 3.1.6.27

L


lab members 9 Lee the whaco's Bfac makeup 5.2
lab research 2 Li 3.1.6.62
large-scale rearrangements 3.1.6.43 ligand 2.3.1
Lars Brive 9.1.4 Long Pentraxins 3.1.6.41
lead compound 2.3.1 lysozyme-antibody complex with 1
Lead Generation 3.1.6.75     6 accuracy 3.1.6.32
leader 9.1, 9.1.1

M


Magnus Berg 9.2.10 modeling homology 2.4.3
mainchain trace 3.1.6.25 Modelling 3.1.6.10, 3.1.6.11
Maiorov 3.1.6.43, 3.1.6.56 models via conformational search 3.1.6.49
major groove of duplex RNA 3.1.6.71 MOID 3.1.6.81
Mammalian Homologue Apaf-1 3.1.6.54 Molecular 3.1.6.3
Mapping 3.1.6.44 Molecular Cellular Biology 3.1.6.62
Mapping regions 3.1.6.47 Molecular docking programs 3.1.6.40
Match-Only 3.1.6.81 molecular modeling 2.1, 3.1.1
Mathieu 3.1.6.53 Molecular Modeling 3.1.6.54
Matthieu Schapira 9.2.3 molecules 3.1.6.2
Maxim Totrov 9.2.1 monomeric triosephosphate isomerase 3.1.6.31, 3.1.6.42
Mazur 3.1.6.10, 3.1.6.18 monoTIM 3.1.6.24, 3.1.6.35, 3.1.6.42
meetings 12 Monte Carlo 3.1.6.60
methods 2.4, 2.4.3, 3.1.4 Monte Carlo Calculations 3.1.6.16
Modeling 3.1.6.76 mutagenesis 3.1.6.76

N


Nature 3.1.6.8 Norledge 3.1.6.76
Nature Genetics 3.1.6.48 novel co-activator mediating functional specificity 3.1.6.62
Nature Struct Biol 3.1.6.40 novel nuclear hormone receptor antagonists 3.1.6.73
Nature Structural Biology 3.1.6.32 novel Retinoic Acid Receptor Agonist Structures 3.1.6.77
new method 3.1.6.33 NRIF3 3.1.6.62
new method modeling 3.1.6.43 Nucl Acids Res 3.1.6.15, 3.1.6.17
New Methodology 3.1.6.10 nuclear hormone receptors 3.1.6.62
new substrate specificity 3.1.6.76

O


Oligo 3.1.6.16, 3.1.6.9 Optimal Protocol 3.1.6.19
Oligonucleotide 3.1.6.81 optimal-bias Monte Carlo minimization 3.1.6.60
oligopeptides 3.1.6.22

P


packing 3.1.6.2 principal investigator 9.1
packing optimization 3.1.6.21 problem 3.1.6.5
papers 3 Proc Natl Acad Sci USA 3.1.6.31
Patel 3.1.6.55 processing 8
people 9 professor 9.1, 9.1.1
peptide 3.1.6.64 properties 3.1.6.8
peptides 3.1.6.60 Proposed structure 3.1.6.26
Peptides and Proteins 3.1.6.19 protein design 2.4.2
peptides and proteins 3.1.6.20 protein domains 3.1.6.43
Peptides and Proteins 3.1.6.30 Protein Eng 3.1.6.42
peptides and proteins 3.1.6.63 Protein Engineering 3.1.6.26, 3.1.6.36
Petukhov 3.1.6.22 Protein engineering 3.1.6.42
PH domain-containing targets phosphatidylinositol 3-kinase 3.1.6.57 protein folding 3.1.6.60
phosphotyrosine-containing peptides bind 3.1.6.58 protein folding problem 3.1.6.29
photo 4 protein modeling 2.4.2
pi 9.1, 9.1.1 protein modeling and design 3.1.6.33
pictures 4 protein models 3.1.6.46
PLoS 11 Protein Science 3.1.6.52
PNAS 3.1.6.73 Protein structure prediction 3.1.6.51
point mutation variants 3.1.6.35 protein structure prediction 3.1.6.67
Polypeptid 3.1.6.7 Protein Tertiary Structures 3.1.6.7
Polypeptides 3.1.6.14 protein- 2.3.1
polypeptides designed 3.1.6.36 Protein-ligand docking 3.1.6.78
polytripeptides 3.1.6.5 Protein-Protein 3.1.6.80, 3.1.6.82
post-doctoral fellowships 9.3 Proteins 3.1.6.13, 3.1.6.28, 3.1.6.43, 3.1.6.49, 3.1.6.50, 3.1.6.76
postdoc 9.1.10, 9.1.11, 9.1.2, 9.1.3, 9.1.5, 9.1.6, 9.1.7, 9.1.8, 9.1.9 Proteins Structure Function Genetics 3.1.6.37
postsynaptic 3.1.6.59 Public Library of Science Initiative 11
prediction 2.2.1, 3.1.6.21 publications 3
Prediction 3.1.6.63

Q


Quantitative 3.1.6.7

R


Rapid boundary element solvation electrostatics calculations 3.1.6.79 ref 48 3.1.6.48
Rashin 3.1.6.52 ref 49 3.1.6.49
Rational discovery 3.1.6.73 ref 5 3.1.6.5
Reaction Mechanism 3.1.6.53 ref 50 3.1.6.50
receptor 3.1.6.59 ref 51 3.1.6.51
recognition 2.2.1 ref 52 3.1.6.52
Recognition 3.1.6.28 ref 53 3.1.6.53
ref 1 3.1.6.1 ref 54 3.1.6.54
ref 10 3.1.6.10 ref 55 3.1.6.55
ref 11 3.1.6.11 ref 56 3.1.6.56
ref 12 3.1.6.12 ref 57 3.1.6.57
ref 13 3.1.6.13 ref 58 3.1.6.58
ref 14 3.1.6.14 ref 59 3.1.6.59
ref 15 3.1.6.15 ref 6 3.1.6.6
ref 16 3.1.6.16 ref 60 3.1.6.60
ref 17 3.1.6.17 ref 61 3.1.6.61
ref 18 3.1.6.18 ref 62 3.1.6.62
ref 19 3.1.6.19 ref 63 3.1.6.63
ref 2 3.1.6.2 ref 64 3.1.6.64
ref 20 3.1.6.20 ref 65 3.1.6.65
ref 21 3.1.6.21 ref 66 3.1.6.66
ref 22 3.1.6.22 ref 67 3.1.6.67
ref 23 3.1.6.23 ref 68 3.1.6.68
ref 24 3.1.6.24 ref 69 3.1.6.69
ref 25 3.1.6.25 ref 7 3.1.6.7
ref 26 3.1.6.26 ref 70 3.1.6.70
ref 27 3.1.6.27 ref 71 3.1.6.71
ref 28 3.1.6.28 ref 72 3.1.6.72
ref 29 3.1.6.29 ref 73 3.1.6.73
ref 3 3.1.6.3 ref 74 3.1.6.74
ref 30 3.1.6.30 ref 75 3.1.6.75
ref 31 3.1.6.31 ref 76 3.1.6.76
ref 32 3.1.6.32 ref 77 3.1.6.77
ref 33 3.1.6.33 ref 78 3.1.6.78
ref 34 3.1.6.34 ref 79 3.1.6.79
ref 35 3.1.6.35 ref 8 3.1.6.8
ref 36 3.1.6.36 ref 80 3.1.6.80
ref 37 3.1.6.37 ref 81 3.1.6.81
ref 38 3.1.6.38 ref 82 3.1.6.82
ref 39 3.1.6.39 ref 9 3.1.6.9
ref 4 3.1.6.4 references 3.1.1, 3.1.2, 3.1.3, 3.1.4, 3.1.6
ref 40 3.1.6.40 replaced active cysteine 3.1.6.48
ref 41 3.1.6.41 Research 2
ref 42 3.1.6.42 research associates 9.1, 9.2
ref 43 3.1.6.43 resumed list 3.1
ref 44 3.1.6.44 Rigidity Theory and Application 3.1.6.67
ref 45 3.1.6.45 robust measure 3.1.6.46
ref 46 3.1.6.46 Ruben Abagyan 9.1.1
ref 47 3.1.6.47

S


Saccharomyces cerevisiae 3.1.6.53 Soft docking 3.1.6.64
Schapira 3.1.6.63, 3.1.6.73, 3.1.6.77 species selective activity 3.1.6.47
scheme 4 Srivastava 3.1.6.59
science 2 Stable Bending 3.1.6.9
screen image 3.1.6.27 staff 9
Second-generation octarellins 3.1.6.36 Stigler 3.1.6.64
sensitive discrimination potential 3.1.6.65 Strands 3.1.6.12
Sequence alignment 2.4.1 Structural 3.1.6.9
Sequence dependent modulating effects 3.1.6.17 Structural Alignment Database 5.1
Sergei Batalov 9.2.6 Structural Relationship 3.1.6.54
servers 5 structural studies 3.1.6.76
services 5 Structure 3.1.6.16, 3.1.6.24, 3.1.6.35, 3.1.6.64
seven residue loop 3.1.6.42 structure prediction 3.1.6.60
SH2 and PTB domains 3.1.6.58 structure verification 3.1.6.42
share same fold 3.1.6.45 structures 3.1.6.4
Sheila Silverstein 9.2.8 Strynadka 3.1.6.40
side-chain conformation 3.1.6.21 submission 5
sign 3.1.6.1 Substrate Binding 3.1.6.53
signal detection 2.4.1 Successful folding 3.1.6.79
Similar Spatial Arrangements 3.1.6.12 successfully predict the binding of a beta-lactamase inhibitory protein 3.1.6.40
Simple 3.1.6.7 support 2.5
small molecule 2.3.1 surface 3.1.6.34
Soft 3.1.6.80, 3.1.6.82

T


tasks 5 Tim Cardozo 9.2.4
technique 3.1.6.27 TNF-a 3.1.6.55
TEM-1 beta-lactamase 3.1.6.40 Tomko 3.1.6.74
Testing 3.1.6.18 tools 5
Thanki 3.1.6.42 Totrov 3.1.6.32, 3.1.6.34, 3.1.6.38, 3.1.6.50, 3.1.6.65, 3.1.6.78, 3.1.6.79
Theoretical Experimental Applications 3.1.6.51 Towards protein folding 3.1.6.23
Therese Eneqvist 9.1.6 Trajectory Visualization 3.1.6.19
thermodynamic electrostatic forces that govern recognition 3.1.6.71 triosephosphate isomerase 3.1.6.76
Thiolase 3.1.6.53 tripeptide 3.1.6.4
Threading and energy profiles 2.2.1 Tumanyan 3.1.6.5
Three new crystal structures 3.1.6.35 tunnel algorithm 3.1.6.22
three-dimensional protein structures 3.1.6.56

U


Unite 6 unite 6.3

V


variable 3.1.6.1 volume 3.1.6.39
virtual ligand screening 3.1.6.65 Vsevolod Katritch 9.2.12
Vladimir Maiorov 9.2.7

W


Wen Hwa Lee 9.1.8

Y


Yingyao Zhou 9.2.2 Yu 3.1.6.44, 3.1.6.47