Academics · Demo University

Academic

RankUnknown

As ofnot recorded

DepartmentHarvard Chemistry

UniversityHarvard

FieldChemistry

ORCID0000-0002-4769-2265

Scholarprofile

Totals

Publications100

Citations25,094

h-index94 · Scholar

Citations per year in post—

Years in postno first year on the CV

Coverage

Works with a count100 of 100

Share100%

Top venues 33 venues

The 8 holding the most of these works; 25 more hold at least one.

Proceedings of the National Academy of Scienc…23

Journal of Molecular Biology14

The Journal of Chemical Physics6

Folding and Design5

Physical Review Letters5

PLoS Computational Biology4

Current Opinion in Structural Biology3

Journal of the American Chemical Society3

Publications per year

Works this academic published in each year, by the year each work appeared; an undated work is in no year, and a work two colleagues wrote counts for each of them. The kind, works and year filters decide which works are here at all.

Citations per year

Citations received in each year, from this academic’s verified Scholar profile, which counts every citation to everything they ever wrote: no publication filter reaches this line - not the kinds, not the works switch, not the year window on publication - and no journal weight either. It is a profile total, so it does not match the works listed below.

Publications 100 works

Every work these filters select, most cited first and the works with no count at the end: a work nobody has a figure for is unknown, never a zero to be ranked among the works that have one, and it prints an em dash. Each figure is that work’s own citations - Scholar’s count where there is one, else OpenAlex’s - and is not weighted.

Year	Title	Venue	Kind	Citations
1994	How does a protein fold?	Nature	article	1,354
2019	Common activation mechanism of class A GPCRs	eLife	article	779
1994	Kinetics of protein folding: A lattice model study of the requirements for folding to the native state	Journal of Molecular Biology	article	746
1993	Engineering of stable and fast-folding sequences of model proteins.	Proceedings of the National Academy of Sciences	article	694
1994	Specific nucleus as the transition state for protein folding: evidence from the lattice model	Biochemistry	article	645
1998	On the transition coordinate for protein folding	The Journal of Chemical Physics	article	606
1988	The role of topological constraints in the kinetics of collapse of macromolecules	Journal de physique	article	561
1998	Estimating the entropic cost of self-assembly of multiparticle hydrogen-bonded aggregates based on the cyanuric Acid⊙ melamine lattice	The Journal of Organic Chemistry	article	544
1997	Theoretical studies of protein-folding thermodynamics and kinetics	Current Opinion in Structural Biology	article	522
1994	Proteins with selected sequences fold into unique native conformation	Physical Review Letters	article	516
1999	Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function	Journal of Molecular Biology	article	488
2006	Protein folding thermodynamics and dynamics: where physics, chemistry and biology meet	Chemical Reviews	article	487
2001	Protein folding theory: from lattice to all-atom models	Annual Review of Biophysics and Biomolecular Structure	article	477
2021	Accelerating high-throughput virtual screening through molecular pool-based active learning	Chemical Science	article	428
1989	Formation of unique structure in polypeptide chains: theoretical investigation with the aid of a replica approach	Biophysical Chemistry	article	426
1996	SMoG: de novo design method based on simple, fast, and accurate free energy estimates. 1. Methodology and supporting evidence	Journal of the American Chemical Society	article	422
2007	Protein and DNA sequence determinants of thermophilic adaptation	PLoS Computational Biology	article	419
1991	Protein folding bottlenecks: A lattice Monte Carlo simulation	Physical Review Letters	article	387
1998	Discrete molecular dynamics studies of the folding of a protein-like model	Folding and Design	article	385
1995	A test of lattice protein folding algorithms.	Proceedings of the National Academy of Sciences	article	381
2002	Topological determinants of protein folding	Proceedings of the National Academy of Sciences	article	370
1989	Theory of cooperative transitions in protein molecules. I. Why denaturation of globular protein is a first‐order phase transition	—	article	365
2005	Physics and evolution of thermophilic adaptation	Proceedings of the National Academy of Sciences	article	364
1990	Implications of thermodynamics of protein folding for evolution of primary sequences	Nature	article	364
1996	How to derive a protein folding potential? A new approach to an old problem	Journal of Molecular Biology	article	344
2007	Protein stability imposes limits on organism complexity and speed of molecular evolution	Proceedings of the National Academy of Sciences	article	330
1995	Impact of local and non-local interactions on thermodynamics and kinetics of protein folding	Journal of Molecular Biology	article	324
1993	A new approach to the design of stable proteins	Protein Engineering Design and Selection	article	315
1990	Enumeration of all compact conformations of copolymers with random sequence of links	The Journal of Chemical Physics	article	311
2012	The interface of protein structure, protein biophysics, and molecular evolution	Protein Science	article	273
1996	Chain length scaling of protein folding time	Physical Review Letters	article	267
2002	Small molecule growth 2001 (SMoG2001): An improved knowledge-based scoring function for protein− ligand interactions	Journal of Medicinal Chemistry	article	252
1994	Free energy landscape for protein folding kinetics: intermediates, traps, and multiple pathways in theory and lattice model simulations	The Journal of Chemical Physics	article	252
1998	How evolution makes proteins fold quickly	Proceedings of the National Academy of Sciences	article	250
2011	A biophysical protein folding model accounts for most mutational fitness effects in viruses	Proceedings of the National Academy of Sciences	article	240
2002	Expanding protein universe and its origin from the biological Big Bang	Proceedings of the National Academy of Sciences	article	230
1998	Protein design: a perspective from simple tractable models	Folding and Design	article	219
2002	The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation	Proceedings of the National Academy of Sciences	article	208
2013	Protein quality control acts on folding intermediates to shape the effects of mutations on organismal fitness	Molecular Cell	article	207
2006	On the origin and highly likely completeness of single-domain protein structures	Proceedings of the National Academy of Sciences	article	204
2002	Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism	Journal of Molecular Biology	article	202
2001	Understanding hierarchical protein evolution from first principles	Journal of Molecular Biology	article	201
1995	Is burst hydrophobic collapse necessary for protein folding?	Biochemistry	article	201
1989	Frozen states of a disordered globular heteropolymer	Journal of Physics A Mathematical and General	article	201
1989	Theory of cooperative transitions in protein molecules. II. Phase diagram for a protein molecule in solution	—	article	197
2000	Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus	Nature Structural Biology	article	193
1989	Formation of microdomains in a quenched disordered heteropolymer	Journal de physique	article	192
2020	Dynamic metastable long-living droplets formed by sticker-spacer proteins	eLife	article	190
2000	Identifying the protein folding nucleus using molecular dynamics	Journal of Molecular Biology	article	185
1995	Evolution-like selection of fast-folding model proteins.	Proceedings of the National Academy of Sciences	article	176
2007	The folding mechanics of a knotted protein	Journal of Molecular Biology	article	173
2001	The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation	Journal of Molecular Biology	article	173
2001	Evolutionary conservation of the folding nucleus	Journal of Molecular Biology	article	172
2016	Biophysical principles predict fitness landscapes of drug resistance	Proceedings of the National Academy of Sciences	article	167
2007	Positive and negative design in stability and thermal adaptation of natural proteins	PLoS Computational Biology	article	167
2002	Direct molecular dynamics observation of protein folding transition state ensemble	Biophysical Journal	article	167
1998	Using a convenient, quantitative model for torsional entropy to establish qualitative trends for molecular processes that restrict conformational freedom	The Journal of Organic Chemistry	article	167
1999	Evidence for the role of PrPC helix 1 in the hydrophilic seeding of prion aggregates	Proceedings of the National Academy of Sciences	article	161
2000	What can disulfide bonds tell us about protein energetics, function and folding: simulations and bioninformatics analysis	Journal of Molecular Biology	article	160
1993	Phase diagram of random copolymers	Physical Review E	article	160
2009	All-atom model for stabilization of α-helical structure in peptides by hydrocarbon staples	Journal of the American Chemical Society	article	154
2003	Structural determinant of protein designability	Physical Review Letters	article	153
1996	Universality and diversity of the protein folding scenarios: a comprehensive analysis with the aid of a lattice model	Folding and Design	article	145
2007	Structural similarity enhances interaction propensity of proteins	Journal of Molecular Biology	article	143
2006	A simple physical model for scaling in protein-protein interaction networks	Proceedings of the National Academy of Sciences	article	137
1997	SMoG: de novo design method based on simple, fast, and accurate free energy estimates. 2. Case studies in molecular design	Journal of the American Chemical Society	article	134
1989	The Nonergodic (“Spin-Glass–Like”) Phase of Heteropolymer with Quenched Disordered Sequence of Links	—	article	131
2001	Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations	Proceedings of the National Academy of Sciences	article	130
2010	De novo design: balancing novelty and confined chemical space	—	article	126
2005	Entropic stabilization of proteins and its proteomic consequences	PLoS Computational Biology	article	126
2012	Protein biophysics explains why highly abundant proteins evolve slowly	Cell Reports	article	124
2017	Evidence of evolutionary selection for cotranslational folding	Proceedings of the National Academy of Sciences	article	123
2008	Constraints imposed by non-functional protein–protein interactions on gene expression and proteome size	Molecular Systems Biology	article	123
2002	Combinatorial computational method gives new picomolar ligands for a known enzyme	Proceedings of the National Academy of Sciences	article	123
2012	Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations	Proceedings of the National Academy of Sciences	article	122
2003	Natural selection of more designable folds: a mechanism for thermophilic adaptation	Proceedings of the National Academy of Sciences	article	119
2022	Excited state non-adiabatic dynamics of large photoswitchable molecules using a chemically transferable machine learning potential	Nature Communications	article	118
2011	Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions	Proceedings of the National Academy of Sciences	article	117
2018	Differential enzyme flexibility probed using solid-state nanopores	ACS Nano	article	116
2003	Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases	Proceedings of the National Academy of Sciences	article	114
2007	All-atom ab initio folding of a diverse set of proteins	Structure	article	113
2005	Protein structure and evolutionary history determine sequence space topology	Genome Research	article	109
2014	Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics	Current Opinion in Structural Biology	article	104
1998	Temperature dependence of the folding rate in a simple protein model: search for a “glass” transition	The Journal of Chemical Physics	article	103
1996	Modelling protein folding: the beauty and power of simplicity	Folding and Design	article	102
2009	FOG: Fragment Optimized Growth Algorithm for the de Novo Generation of Molecules Occupying Druglike Chemical Space	Journal of Chemical Information and Modeling	article	101
1996	Adsorption-freezing transition for random heteropolymers near disordered 2D manifolds due to “pattern matching”	Physical Review Letters	article	100
1996	Improved design of stable and fast-folding model proteins	Folding and Design	article	99
2005	Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations	Journal of Molecular Biology	article	97
1994	Statistical mechanics of proteins with ‘‘evolutionary selected’’sequences	Physical Review E	article	97
1994	Pseudodihedrals: simplified protein backbone representation with knowledge‐based energy	Protein Science	article	97
1993	Ground state of random copolymers and the discrete random energy model	The Journal of Chemical Physics	article	97
1998	Folding and misfolding of designed proteinlike chains with mutations	The Journal of Chemical Physics	article	96
2010	Optimality of mutation and selection in germinal centers	PLoS Computational Biology	article	95
2015	Protein homeostasis imposes a barrier on functional integration of horizontally transferred genes in bacteria	PLoS Genetics	article	92
2007	Robust protein–protein interactions in crowded cellular environments	Proceedings of the National Academy of Sciences	article	92
2004	Commitment and nucleation in the protein G transition state	Journal of Molecular Biology	article	92
2002	A structure-based method for derivation of all-atom potentials for protein folding	Proceedings of the National Academy of Sciences	article	91
2017	Bridging the physical scales in evolutionary biology: from protein sequence space to fitness of organisms and populations	Current Opinion in Structural Biology	article	90
2016	OpenGrowth: an automated and rational algorithm for finding new protein ligands	Journal of Medicinal Chemistry	article	88

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