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Point Process Analysis of Noise in Early Invertebrate Vision
Noise is a prevalent and sometimes even dominant aspect of many biological processes. While many natural systems have adapted to attenuate or even usefully integrate noise, the variability it introduces often still delimits the achievable precision across biological functions. This is particularly so for visual phototransduction, the process responsible for converting photons of light into usable electrical signals (quantum bumps). Here, randomness of both the photon inputs (regarded as extrinsic noise) and the conversion process (intrinsic noise) are seen as two distinct, independent and significant limitations on visual reliability. Past research has attempted to quantify the relative effects of these noise sources by using approximate methods that do not fully account for the discrete, point process and time ordered nature of the problem. As a result the conclusions drawn from these different approaches have led to inconsistent expositions of phototransduction noise performance. This paper provides a fresh and complete analysis of the relative impact of intrinsic and extrinsic noise in invertebrate phototransduction using minimum mean squared error reconstruction techniques based on Bayesian point process (Snyder) filters. An integrate-fire based algorithm is developed to reliably estimate photon times from quantum bumps and Snyder filters are then used to causally estimate random light intensities both at the front and back end of the phototransduction cascade. Comparison of these estimates reveals that the dominant noise source transitions from extrinsic to intrinsic as light intensity increases. By extending the filtering techniques to account for delays, it is further found that among the intrinsic noise components, which include bump latency (mean delay and jitter) and shape (amplitude and width) variance, it is the mean delay that is critical to noise performance. Consequently, if one wants to increase visual fidelity, reducing the photoconversion lag is much more important than improving the regularity of the electrical signal.This work was supported by the Gates Cambridge Trust (PhD studentship for research) https://www.gatescambridge.org/. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
Develop and Test a Solvent Accessible Surface Area-Based Model in Conformational Entropy Calculations
It is of great interest in modern drug design to accurately
calculate the free energies of protein–ligand or nucleic acid–ligand
binding. MM-PBSA (molecular mechanics Poisson–Boltzmann surface
area) and MM-GBSA (molecular mechanics generalized Born surface area)
have gained popularity in this field. For both methods, the conformational
entropy, which is usually calculated through normal-mode analysis
(NMA), is needed to calculate the absolute binding free energies.
Unfortunately, NMA is computationally demanding and becomes a bottleneck
of the MM-PB/GBSA-NMA methods. In this work, we have developed a fast
approach to estimate the conformational entropy based upon solvent
accessible surface area calculations. In our approach, the conformational
entropy of a molecule, <i>S</i>, can be obtained by summing
up the contributions of all atoms, no matter they are buried or exposed.
Each atom has two types of surface areas, solvent accessible surface
area (SAS) and buried SAS (BSAS). The two types of surface areas are
weighted to estimate the contribution of an atom to <i>S</i>. Atoms having the same atom type share the same weight and a general
parameter <i>k</i> is applied to balance the contributions
of the two types of surface areas. This entropy model was parametrized
using a large set of small molecules for which their conformational
entropies were calculated at the B3LYP/6-31G* level taking the solvent
effect into account. The weighted solvent accessible surface area
(WSAS) model was extensively evaluated in three tests. For convenience, <i><i>TS</i></i> values, the product of temperature <i>T</i> and conformational entropy <i>S</i>, were calculated
in those tests. <i>T</i> was always set to 298.15 K through
the text. First of all, good correlations were achieved between WSAS <i>TS</i> and NMA <i>TS</i> for 44 protein or nucleic
acid systems sampled with molecular dynamics simulations (10 snapshots
were collected for postentropy calculations): the mean correlation
coefficient squares (<i>R</i><sup>2</sup>) was 0.56. As
to the 20 complexes, the <i>TS</i> changes upon binding; <i>T</i>Δ<i>S</i> values were also calculated,
and the mean <i>R</i><sup>2</sup> was 0.67 between NMA and
WSAS. In the second test, <i>TS</i> values were calculated
for 12 proteins decoy sets (each set has 31 conformations) generated
by the Rosetta software package. Again, good correlations were achieved
for all decoy sets: the mean, maximum, and minimum of <i>R</i><sup>2</sup> were 0.73, 0.89, and 0.55, respectively. Finally, binding
free energies were calculated for 6 protein systems (the numbers of
inhibitors range from 4 to 18) using four scoring functions. Compared
to the measured binding free energies, the mean <i>R</i><sup>2</sup> of the six protein systems were 0.51, 0.47, 0.40, and
0.43 for MM-GBSA-WSAS, MM-GBSA-NMA, MM-PBSA-WSAS, and MM-PBSA-NMA,
respectively. The mean rms errors of prediction were 1.19, 1.24, 1.41,
1.29 kcal/mol for the four scoring functions, correspondingly. Therefore,
the two scoring functions employing WSAS achieved a comparable prediction
performance to that of the scoring functions using NMA. It should
be emphasized that no minimization was performed prior to the WSAS
calculation in the last test. Although WSAS is not as rigorous as
physical models such as quasi-harmonic analysis and thermodynamic
integration (TI), it is computationally very efficient as only surface
area calculation is involved and no structural minimization is required.
Moreover, WSAS has achieved a comparable performance to normal-mode
analysis. We expect that this model could find its applications in
the fields like high throughput screening (HTS), molecular docking,
and rational protein design. In those fields, efficiency is crucial
since there are a large number of compounds, docking poses, or protein
models to be evaluated. A list of acronyms and abbreviations used
in this work is provided for quick reference
Develop and Test a Solvent Accessible Surface Area-Based Model in Conformational Entropy Calculations
It is of great interest in modern drug design to accurately
calculate the free energies of protein–ligand or nucleic acid–ligand
binding. MM-PBSA (molecular mechanics Poisson–Boltzmann surface
area) and MM-GBSA (molecular mechanics generalized Born surface area)
have gained popularity in this field. For both methods, the conformational
entropy, which is usually calculated through normal-mode analysis
(NMA), is needed to calculate the absolute binding free energies.
Unfortunately, NMA is computationally demanding and becomes a bottleneck
of the MM-PB/GBSA-NMA methods. In this work, we have developed a fast
approach to estimate the conformational entropy based upon solvent
accessible surface area calculations. In our approach, the conformational
entropy of a molecule, <i>S</i>, can be obtained by summing
up the contributions of all atoms, no matter they are buried or exposed.
Each atom has two types of surface areas, solvent accessible surface
area (SAS) and buried SAS (BSAS). The two types of surface areas are
weighted to estimate the contribution of an atom to <i>S</i>. Atoms having the same atom type share the same weight and a general
parameter <i>k</i> is applied to balance the contributions
of the two types of surface areas. This entropy model was parametrized
using a large set of small molecules for which their conformational
entropies were calculated at the B3LYP/6-31G* level taking the solvent
effect into account. The weighted solvent accessible surface area
(WSAS) model was extensively evaluated in three tests. For convenience, <i><i>TS</i></i> values, the product of temperature <i>T</i> and conformational entropy <i>S</i>, were calculated
in those tests. <i>T</i> was always set to 298.15 K through
the text. First of all, good correlations were achieved between WSAS <i>TS</i> and NMA <i>TS</i> for 44 protein or nucleic
acid systems sampled with molecular dynamics simulations (10 snapshots
were collected for postentropy calculations): the mean correlation
coefficient squares (<i>R</i><sup>2</sup>) was 0.56. As
to the 20 complexes, the <i>TS</i> changes upon binding; <i>T</i>Δ<i>S</i> values were also calculated,
and the mean <i>R</i><sup>2</sup> was 0.67 between NMA and
WSAS. In the second test, <i>TS</i> values were calculated
for 12 proteins decoy sets (each set has 31 conformations) generated
by the Rosetta software package. Again, good correlations were achieved
for all decoy sets: the mean, maximum, and minimum of <i>R</i><sup>2</sup> were 0.73, 0.89, and 0.55, respectively. Finally, binding
free energies were calculated for 6 protein systems (the numbers of
inhibitors range from 4 to 18) using four scoring functions. Compared
to the measured binding free energies, the mean <i>R</i><sup>2</sup> of the six protein systems were 0.51, 0.47, 0.40, and
0.43 for MM-GBSA-WSAS, MM-GBSA-NMA, MM-PBSA-WSAS, and MM-PBSA-NMA,
respectively. The mean rms errors of prediction were 1.19, 1.24, 1.41,
1.29 kcal/mol for the four scoring functions, correspondingly. Therefore,
the two scoring functions employing WSAS achieved a comparable prediction
performance to that of the scoring functions using NMA. It should
be emphasized that no minimization was performed prior to the WSAS
calculation in the last test. Although WSAS is not as rigorous as
physical models such as quasi-harmonic analysis and thermodynamic
integration (TI), it is computationally very efficient as only surface
area calculation is involved and no structural minimization is required.
Moreover, WSAS has achieved a comparable performance to normal-mode
analysis. We expect that this model could find its applications in
the fields like high throughput screening (HTS), molecular docking,
and rational protein design. In those fields, efficiency is crucial
since there are a large number of compounds, docking poses, or protein
models to be evaluated. A list of acronyms and abbreviations used
in this work is provided for quick reference
P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape
<div><p>Tyrosine kinases are regarded as excellent targets for chemical drug therapy of carcinomas. However, under strong purifying selection, drug resistance usually occurs in the cancer cells within a short term. Many cases of drug resistance have been found to be associated with secondary mutations in drug target, which lead to the attenuated drug-target interactions. For example, recently, an acquired secondary mutation, G2032R, has been detected in the drug target, ROS1 tyrosine kinase, from a crizotinib-resistant patient, who responded poorly to crizotinib within a very short therapeutic term. It was supposed that the mutation was located at the solvent front and might hinder the drug binding. However, a different fact could be uncovered by the simulations reported in this study. Here, free energy surfaces were characterized by the drug-target distance and the phosphate-binding loop (P-loop) conformational change of the crizotinib-ROS1 complex through advanced molecular dynamics techniques, and it was revealed that the more rigid P-loop region in the G2032R-mutated ROS1 was primarily responsible for the crizotinib resistance, which on one hand, impaired the binding of crizotinib directly, and on the other hand, shortened the residence time induced by the flattened free energy surface. Therefore, both of the binding affinity and the drug residence time should be emphasized in rational drug design to overcome the kinase resistance.</p></div
Drug-likeness Analysis of Traditional Chinese Medicines: Prediction of Drug-likeness Using Machine Learning Approaches
Quantitative or qualitative characterization of the drug-like
features
of known drugs may help medicinal and computational chemists to select
higher quality drug leads from a huge pool of compounds and to improve
the efficiency of drug design pipelines. For this purpose, the theoretical
models for drug-likeness to discriminate between drug-like and non-drug-like
based on molecular physicochemical properties and structural fingerprints
were developed by using the naive Bayesian classification (NBC) and
recursive partitioning (RP) techniques, and then the drug-likeness
of the compounds from the Traditional Chinese Medicine Compound Database
(TCMCD) was evaluated. First, the impact of molecular physicochemical
properties and structural fingerprints on the prediction accuracy
of drug-likeness was examined. We found that, compared with simple
molecular properties, structural fingerprints were more essential
for the accurate prediction of drug-likeness. Then, a variety of Bayesian
classifiers were constructed by changing the ratio of drug-like to
non-drug-like molecules and the size of the training set. The results
indicate that the prediction accuracy of the Bayesian classifiers
was closely related to the size and the degree of the balance of the
training set. When a balanced training set was used, the best Bayesian
classifier based on 21 physicochemical properties and the LCFP_6 fingerprint
set yielded an overall leave-one-out (LOO) cross-validated accuracy
of 91.4% for the 140,000 molecules in the training set and 90.9% for
the 40,000 molecules in the test set. In addition, the RP classifiers
with different maximum depth were constructed and compared with the
Bayesian classifiers, and we found that the best Bayesian classifier
outperformed the best RP model with respect to overall prediction
accuracy. Moreover, the Bayesian classifier employing structural fingerprints
highlights the important substructures favorable or unfavorable for
drug-likeness, offering extra valuable information for getting high
quality lead compounds in the early stage of the drug design/discovery
process. Finally, the best Bayesian classifier was used to predict
the drug-likeness of 33,961 compounds in TCMCD. Our calculations show
that 59.37% of the molecules in TCMCD were identified as drug-like
molecules, indicating that traditional Chinese medicines (TCMs) are
therefore an excellent source of drug-like molecules. Furthermore,
the important structural fingerprints in TCMCD were detected and analyzed.
Considering that the pharmacology of TCMCD and MDDR (MDL Drug Data
Report) was linked by the important common structural features, the
potential pharmacology of the compounds in TCMCD may therefore be
annotated by these important structural signatures identified from
Bayesian analysis, which may be valuable to promote the development
of TCMs
Assessing the Performance of MM/PBSA and MM/GBSA Methods. 3. The Impact of Force Fields and Ligand Charge Models
Here,
we systematically investigated how the force fields and the
partial charge models for ligands affect the ranking performance of
the binding free energies predicted by the Molecular Mechanics/Poisson–Boltzmann
Surface Area (MM/PBSA) and Molecular Mechanics/Generalized Born Surface
Area (MM/GBSA) approaches. A total of 46 small molecules targeted
to five different protein receptors were employed to test the following
issues: (1) the impact of five AMBER force fields (ff99, ff99SB, ff99SB-ILDN,
ff03, and ff12SB) on the performance of MM/GBSA, (2) the influence
of the time scale of molecular dynamics (MD) simulations on the performance
of MM/GBSA with different force fields, (3) the impact of five AMBER
force fields on the performance of MM/PBSA, and (4) the impact of
four different charge models (RESP, ESP, AM1-BCC, and Gasteiger) for
small molecules on the performance of MM/PBSA or MM/GBSA. Based on
our simulation results, the following important conclusions can be
obtained: (1) for short time-scale MD simulations (1 ns or less),
the ff03 force field gives the best predictions by both MM/GBSA and
MM/PBSA; (2) for middle time-scale MD simulations (2–4 ns),
MM/GBSA based on the ff99 force field yields the best predictions,
while MM/PBSA based on the ff99SB force field does the best; however,
longer MD simulations, for example, 5 ns or more, may not be quite
necessary; (3) for most cases, MM/PBSA with the Tan’s parameters
shows better ranking capability than MM/GBSA (GB<sup>OBC1</sup>);
(4) the RESP charges show the best performance for both MM/PBSA and
MM/GBSA, and the AM1-BCC and ESP charges can also give fairly satisfactory
predictions. Our results provide useful guidance for the practical
applications of the MM/GBSA and MM/PBSA approaches
Discovery of Potent and Selective CB2 Agonists Utilizing a Function-Based Computational Screening Protocol
Nowadays, the identification of agonists and antagonists
represents
a great challenge in computer-aided drug design. In this work, we
developed a computational protocol enabling us to design/screen novel
chemicals that are likely to serve as selective CB2 agonists. The
principle of this protocol is that by calculating the ligand–residue
interaction profile (LRIP) of a ligand binding to a specific target,
the agonist–antagonist function of a compound is then able
to be determined after statistical analysis and free energy calculations.
This computational protocol was successfully applied in CB2 agonist
development starting from a lead compound, and a success rate of 70%
was achieved. The functions of the synthesized derivatives were determined
by in vitro functional assays. Moreover, the identified potent CB2
agonists and antagonists strongly interact with the key residues identified
using the already known potent CB2 agonists/antagonists. The analysis
of the interaction profile of compound 6, a potent agonist,
showed strong interactions with F2.61, I186, and F2.64, while compound 39, a potent antagonist, showed strong interactions with L17,
W6.48, V6.51, and C7.42. Still, some residues including V3.32, T3.33,
S7.39, F183, W5.43, and I3.29 are hotspots for both CB2 agonists and
antagonists. More significantly, we identified three hotspot residues
in the loop, including I186 for agonists, L17 for antagonists, and
F183 for both. These hotspot residues are typically not considered
in CB1/CB2 rational ligand design. In conclusion, LRIP is a useful
concept in rationally designing a compound to possess a certain function
The most populated bound-state conformations (averaged structures) and dihedral angle distributions of the P-loop region in WT-ROS1 (gray, panel A) and G2032R-ROS1 (purple, panel B).
<p>The dihedral angle was calculated by C<sub>α</sub> of the residues 20, 22, 25 and 150 (the index of the residues were renumbered from 1 to 285) in panels C–F. The mutated site G2032R, P-loop region, and crizotinib in WT-ROS1 and G2032R-ROS1 are shown in green surface, orange surface, green stick, and pink stick models, respectively, in panels A and B. The dihedral angle distributions are colored in grey, orange, purple, and green in bound-state WT-ROS1, free-state WT-ROS1, bound-state G2032R-ROS1, and free-state G2032R-ROS1, respectively.</p
Discovery of Potent and Selective CB2 Agonists Utilizing a Function-Based Computational Screening Protocol
Nowadays, the identification of agonists and antagonists
represents
a great challenge in computer-aided drug design. In this work, we
developed a computational protocol enabling us to design/screen novel
chemicals that are likely to serve as selective CB2 agonists. The
principle of this protocol is that by calculating the ligand–residue
interaction profile (LRIP) of a ligand binding to a specific target,
the agonist–antagonist function of a compound is then able
to be determined after statistical analysis and free energy calculations.
This computational protocol was successfully applied in CB2 agonist
development starting from a lead compound, and a success rate of 70%
was achieved. The functions of the synthesized derivatives were determined
by in vitro functional assays. Moreover, the identified potent CB2
agonists and antagonists strongly interact with the key residues identified
using the already known potent CB2 agonists/antagonists. The analysis
of the interaction profile of compound 6, a potent agonist,
showed strong interactions with F2.61, I186, and F2.64, while compound 39, a potent antagonist, showed strong interactions with L17,
W6.48, V6.51, and C7.42. Still, some residues including V3.32, T3.33,
S7.39, F183, W5.43, and I3.29 are hotspots for both CB2 agonists and
antagonists. More significantly, we identified three hotspot residues
in the loop, including I186 for agonists, L17 for antagonists, and
F183 for both. These hotspot residues are typically not considered
in CB1/CB2 rational ligand design. In conclusion, LRIP is a useful
concept in rationally designing a compound to possess a certain function
Additional file 1 of Association of gallbladder diseases with risk of gastrointestinal polyps
Additional file 1
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